New York Seagrass Experts Meeting

Home , Codium fragile, Shelter Island Sound, South Oyster Bay, South Shore Estuary

Meeting Proceedings and Priority Recommendations

May 22, 2007 Photo by: Cornell Cooperative Extension of Suffolk County Marine Program East Setauket, NY

Acknowledgements

This meeting was sponsored by the New York State Department of Environmental Conservation, New York Sea Grant, Peconic Estuary Program, Cornell Cooperative Extension, The Nature Conservancy and the Long Island Sound Study.

A special thank you to members of the Steering Committee for their many months of strategic planning, and the Experts Panel for their unsurpassed dedication and enthusiasm.

Table of Contents

Introduction 1

Workshop Format 2

Agenda 4

Appendix A: New York State Seagrass Taskforce Legislation 6

Appendix B: Expert Panel Bios 10

Appendix C: Presenter Bios 14

Appendix D: List of Meeting Attendees 17

Appendix E: Presentation Abstracts/Slides 20

Appendix F: Research, Management, and Monitoring Priorities 68

Appendix G: Pre-Meeting Potential Research Questions 73

Appendix H: Other Supplemental Materials 76 Maps Research Conducted in the Peconic Estuary Regarding Eelgrass Actions and Recommendations Involving Eelgrass in the Peconic Estuary Comprehensive Conservation and Management Plan Local Management Affecting Eelgrass in the Peconic Estuary New York State Management Impacting Eelgrass Long Island Estuary Systems: Snapshot

Introduction Seagrasses are rooted, underwater vascular plants which grow in shallow coastal waters. While several different species of seagrasses exist, the two most commonly found species in New York’s coastal waters are eelgrass (Zostera marina) and widgeon grass (Ruppia maritime). These submerged aquatic vegetation (SAV’s), are considered to be some of the most productive ecosystems in the world and are biologically, ecologically and economically important. Seagrass beds stabilize benthic sediments, support nutrient cycling, oxygenate waters, improve water quality, and provide critical habitat for aquatic species (e.g., fluke, bluefish, bay scallops and hard clams). The presence of seagrass is often used as an indicator of estuarine health and high water quality.

Long Island marine waters once supported bountiful populations of seagrass. The onset of a wasting disease (Labyrinthula zostorae) in the early 1930’s was responsible for the significant decline of eelgrass beds along the entire Atlantic seaboard. Light shading effects of Brown Tide occurrences in the 1980’s further decimated eelgrass populations. Long Island seagrass populations may also continue to be impacted by nutrient enrichment, fishing and shellfishing practices, and recreational use of shallow waterways. Despite management and restoration efforts and significant improvements in water quality, populations are still declining and have not rebounded. Monitoring efforts in Long Island Sound, the Peconic Bays, and the South Shore Estuary indicate that these individual estuarine systems have each experienced separate and distinct trends. If qualitative and quantitative improvements in eelgrass beds are sought, these systems and their respective trends must be examined further.

Acknowledging the importance of seagrass and the necessity to protect and restore this valuable natural resource, Governor George Pataki enacted Chapter 404 of the Laws of 2006 on July 26, 2006, which established a New York Seagrass Task Force within the New York Department of Environmental Conservation. This Task Force is charged with examining the current state and make recommendations on means of restoring, preserving, and properly managing seagrass. Task Force meetings have since commenced in early 2008; the legislation can be found in Appendix A.

In the meantime, several representatives from various agencies and organizations decided to proceed with heightening awareness of declining seagrass trends, and drawing attention to the need of directing resources to foster an increased understanding. Consequently, a Steering Committee was formed. Members included:

Rick Balla, United States Environmental Protection Agency/ Peconic Estuary Program Marci Bortman, The Nature Conservancy Jerry Churchill, Adelphi University Karen Chytalo, NYS Department of Environmental Conservation, Bureau of Marine Resources Corey Garza, National Oceanic and Atmospheric Administration/Long Island Sound Study Jack Mattice, New York Sea Grant Brad Peterson, State University of New York Chris Pickerell, Cornell Cooperative Extension Cornelia Schlenk, New York Sea Grant Laura Stephenson, NYS Department of Environmental Conservation/Peconic Estuary Program

1 This Steering Committee would organize a Seagrass Experts Meeting that would help establish a body of background information look at past and current trends, facilitate discussion between local seagrass experts, and gain insights from nationally renowned seagrass scientists and managers.

Meeting Format The main goal of the Seagrass Experts Meeting was to have a scientific panel of experts reach a consensus about what information gaps would be the most important to fill in order for New York to move forward most efficiently and effectively toward preserving and/or restoring seagrass habitat.

The first step was to establish a panel of seagrass experts. In an attempt to create a diverse panel, individuals were selected based on unique expertise and complementary knowledge and experience. The Steering Committee was extremely fortunate in being able to secure the interest and participation of several key, nationally-recognized seagrass experts; some located on Long Island, while others based in Alabama, Florida, Maryland, New Hampshire and North Carolina (see Figure 1). Brief biographies of Expert Panel members can be found in Appendix B. The Expert Panel was asked to attend a meeting to learn about conditions in New York, synthesis and integrate information through discussion, and then develop recommendations on research, management and monitoring priorities.

Figure 1- Experts Panel (L to R): Paul Carlson (Florida Fish and Wildlife Conservation Commission), Bradley Peterson (Stony Brook University), William Dennison (University of Maryland), Kenneth Heck, Jr., (University of South Alabama), Mark Fonseca (NOAA National Ocean Service), Chris Pickerell (Cornell Cooperative Extension), A. Coolidge Churchill (Adelphi University), Fred Short (University of New Hampshire).

2 The next step was to identify local scientists, researchers, and managers to present the local context and set the stage for the Experts Panel’s deliberations. These individuals were to address the relevant physical, biological, and chemical characteristics of Long Island Sound, the Peconic Bays, and the South Shore Estuary, as well as past and current status of seagrasses in those systems. Brief biographies of those presenters may be found in Appendix C.

The New York Seagrass Experts Meeting was held on May 22, 2007 at the New York State Department of Environmental Conservation Bureau of Marine Resources Headquarters located in East Setauket, New York. To keep the Meeting as focused and productive as possible, invitees were limited essentially to the Steering Committee, the local presenters, and the Experts Panel (see Appendix D). The agenda (see following page) began with presentations of local information to set the stage (see Appendix E for presentation abstracts and slides). Question and answer periods followed, proceeded by Expert Panel deliberations which continued late into the evening. The output of the Expert Panel deliberations was a table of priority actions (see Appendix F) which identifies: • The ranked order of priority; • Whether it is a research, monitoring or management activity; • What the recommended action is; • Tasks to be undertaken to accomplish the action; • An estimate of the time period required; and • An estimate of the costs involved

Expectations of the Steering Committee were well exceeded. An incredible amount of information was shared and valuable new connections between individuals made. Most importantly, priority recommendations reflect those of informed, interested, and impartial experts. Those recommended actions provide a needed, well-founded direction for New York’s future efforts to preserve and restore the seagrass beds of its estuarine waters.

3 AGENDA Seagrass Experts Meeting May 22nd, 2007 NYSDEC Bureau of Marine Resources

8:00am Registration and Continental Breakfast

8:30am Welcome Jack Mattice, Ph.D- Director, NY Sea Grant

Overview of Meeting Karen Chytalo- Section Chief, Marine Habitat Protection, New York State Department of Environmental Conservation, Bureau of Marine Resources

8:45am Snapshot of Long Island Marine Waters: Physical Characteristics Short presentations, each followed by questions/discussion

1. Water Quality-Nutrients, Phytoplankton (approx 8:45-9:00am) Chris Gobler, Ph.D.- Associate Professor, Marine Sciences Research Center, Stony Brook University

2. Linking Groundwater, Pesticides and SAV’s (approx 9:00-9:15am) Ron Paulsen- Hydrogeologist. Suffolk County Department of Health Services, Office of Water Resources

3. Marine Sediment Geo-chemistry (approx 9:15-9:30am) Kirk Cochran, Ph.D.- Professor, Marine Sciences Research Center, Stony Brook University

4. Habitat Modification & Loss of Suspension Feeders (approx 9:30- 9:45am) Brad Peterson, Ph.D.- Assistant Professor, Marine Sciences Research Center, Stony Brook University

9:55am Break Display of current and historical eelgrass maps

10:10am Status, Historical Distributions, and Current Management and Research Approaches

1. South Shore (approx 10:10-10:25am) Chris Clapp- Estuary Specialist, The Nature Conservancy

2. Peconic Estuary (approx 10:25-10:40am) Steve Schott- Marine Botany Educator, Cornell Cooperative Extension Kim Petersen- Habitat Restoration Educator, Cornell Cooperative Extension

4 3. Long Island Sound (approx 10:40-10:55am) Tom Halavik- Senior Biologist, United States Fish and Wildlife Service

11:00am A Brief History of Long Island Restoration Efforts Chris Pickerell- Habitat Restoration Specialist, Cornell Cooperative Extension

11:15am Introduction to Panel Discussion Overview of Panel Discussion and Introduction of Potential Research Questions (see Appendix G) Karen Chytalo- Section Chief, Marine Habitat Protection, New York State Department of Environmental Conservation, Bureau of Marine Resources

11:30am Working Lunch (Provided) Expert Panel will convene with facilitator to discuss presented information Cornelia Schlenk- Assistant Director, NY Sea Grant

12:15pm Expert Panel Questions for Speakers

12:35pm Group Discussion: Discussing Research and Monitoring Priorities

3:15pm Narrowing the Focus and Prioritizing Expert Panel convenes with facilitator to refine and prioritize research and monitoring agenda. Provide timeframes and estimated costs where applicable. Cornelia Schlenk- Assistant Director, NY Sea Grant

4:15pm Meeting Wrap Up- Next Steps Expert Panel will reconvene with group to present and discuss fully developed priorities

4:45pm Adjourn

Appendix A: New York State Seagrass Task Force Legislation

6 NEW YORK STATE SENATE INTRODUCER'S MEMORANDUM IN SUPPORT submitted in accordance with Senate Rule VI. Sec 1

BILL NUMBER: S8052

SPONSOR: JOHNSON¦¦¦¦¦¦¦¦¦¦¦¦¦

TITLE OF BILL: An act to establish a seagrass research, monitoring and restoration task force and providing for its powers and duties; and providing for the repeal of such provisions upon expiration thereof

PURPOSE: To establish a task force that will examine and make recommendations on means of restoring, preserving and properly managing seagrass.

SUMMARY OF PROVISIONS: Section one establishes a seagrass research, monitoring and restoration task force. The Task force will consist of five voting members and ten non-voting members.

Sections two, three and four provide for the organization of the task force by establishing that the chairperson will be the commissioner of environmental conservation or his or her designee and requires that any vacancies on the task force be filled in the manner provided by the initial appointment.

Sections five, six and seven authorize the task force to hold public hearings and meetings to enable it to accomplish its duties; and requires that every state agency, local agency and public corporation having jurisdiction over areas of native seagrass habitat or over programs relating to the purposes and goals of this act offer full cooperation and assistance to the task force in carrying out the provisions of this act. Defines "native seagrass," as native underwater plants found in Long Island bays and estuaries including, but not limited to, eelgrass and widgeon grass.

JUSTIFICATION: Long Island seagrass populations were severely decimated by wasting disease in the 1930s and again by a massive brown tide event in the 1980s. Despite the absence of these events in some areas like the Peconic Bays and Long Island Sound over the past 20 years, local seagrasses have not recovered. The intent of this legislation is to set up a task force to develop recommendations for regulations to improve seagrass protection, restoration, research and monitoring.

This task force will establish the necessary framework for reducing the impact of direct and indirect threats and restoring and properly managing seagrass into the future. Direct impacts include physical damage from boat groundings, incompatible fishing practices, docks and bulkheads, and other potentially destructive activities. Indirect impacts include water quality effects from nutrients, sedimentation and toxic contaminants.

Effective regulations for seagrass protection and restoration will depend greatly on the State's ability to understand the severity of these impacts. This task force will identify and assess severity of indirect and direct

7 threats, develop restoration goals, recommend short-term and long-term research and monitoring and propose public outreach and education tools. Seagrass, which is designated as Essential Fish Habitat and a Habitat Area of Particular Concern for many of New York State's recreationally and commercially important marine species, is a vital component to successful and lasting restoration of Long Island finfish, shellfish, crustacean, and waterfowl populations, which has far reaching benefits for improved quality of life and economic growth opportunities for present and future generations on Long Island.

LEGISLATIVE HISTORY: New bill.

FISCAL IMPLICATIONS: Minimal.

EFFECTIVE DATE: This act shall take effect immediately and be deemed repealed January 1, 2009.

LAWS OF NEW YORK, 2006

CHAPTER 404

AN ACT to establish a seagrass research, monitoring and restoration task force and providing for its powers and duties; and providing for the repeal of such provisions upon expiration thereof

Became a law July 26, 2006, with the approval of the Governor. Passed by a majority vote, three-fifths being present.

The People of the State of New York, represented in Senate and Assembly, do enact as follows:

Section 1. Seagrass research, monitoring and restoration task force. There is hereby established, within the department of environmental conservation a seagrass research, monitoring and restoration task force("task force") which shall consist of five voting members and ten non-voting members who shall be appointed as follows: (a)the commissioner of environmental conservation or his or her designee; (b)the commissioner of parks, recreation and historic preservation or his or her designee; (c)the secretary of state or his or her designee; (d)one member upon the recommendation of the temporary president of the senate; (e)one member upon the recommendation of the speaker of the assembly; (f)ten non-voting members to be selected by the department of environmental conservation representing: recreational anglers, town marine law enforcement, estuary programs, the commercial fishing industry, recreational boaters, the director of New York sea grant, local government officials, the marine resources advisory council, New York businesses and advocates for the environment.

8 § 2. Task force members shall receive no compensation for their services but shall be reimbursed for actual and necessary expenses incurred in the performance of their duties.

§ 3. The chairperson of the task force shall be the commissioner of environmental conservation or his or her designee. The task force shall meet no less than four times and at other times at the call of the chairperson.

§ 4. Any vacancies on the task force shall be filled in the manner provided for in the initial appointment.

§ 5. The task force shall be authorized to hold public hearings and meetings to enable it to accomplish its duties.

§ 6. Every state agency, local agency and public corporation having jurisdiction over areas of native seagrass habitat or over programs relating to the purposes and goals of this act shall, to the fullest extent practicable, offer full cooperation and assistance to the task force in carrying out the provisions of this act.

§ 7. As used in this act, "native seagrass" shall mean native underwater plants found in Long Island bays and estuaries including, but not limited to, eelgrass (zostera marina) and widgeon grass(ruppia maritima); "native seagrass meadows" shall mean those habitats in estuarine waters vegetated with one or more species of native seagrass.

§ 8. No later than December 31, 2008, the task force shall transmit to the governor, the temporary president of the senate and the speaker of the assembly a report containing recommendations on how to accomplish the following: (a) Recommendations on elements of a seagrass management plan including, but not limited to, regulatory and/or statutory alterations required to preserve, restore, protect and map the native seagrass population on Long Island. (b) Recommendations on means of preserving and restoring seagrass and native seagrass meadows that will bring about a lasting restoration of finfish, shellfish, crustaceans, and waterfowl, that is compatible with an improved quality of life and economic growth for the future of the region. Such proposals shall also include any recommendations for monitoring, additional research, and public education to ensure the success of the effort.

§ 9. This act shall take effect immediately and shall expire and be deemed repealed January 1, 2009.

The Legislature of the STATE OF NEW YORK ss: Pursuant to the authority vested in us by section 70-b of the Public Officers Law, we hereby jointly certify that this slip copy of this session law was printed under our direction and, in accordance with such section, is entitled to be read into evidence.

JOSEPH L. BRUNO SHELDON SILVER Temporary President of the Senate Speaker of the Assembly

Appendix B: Expert Panel Bios

10 Brief Biographies of the Seagrass Experts Panel

Paul Carlson received his BA in Biology from New College in Sarasota, FL and his PhD in Ecology from UNC-Chapel Hill. After postdocs at U. Maryland Horn Point Environmental Laboratory and Harbor Branch Oceanographic Institution, he joined the Florida Marine Research Institute as a research scientist in 1984 working on seagrass, mangrove, and salt marsh habitat monitoring, assessment, and restoration. Significant projects have included seagrass mortality in Florida Bay, water quality management in mosquito control impoundments, bioturbation impacts on seagrass beds in Tampa Bay, and seagrass mapping and monitoring in Florida's Big Bend.

A. Coolidge Churchill earned a PhD at the University of Oregon studying marine algae under Richard Castenholz. His first and only full-time job has been at Adelphi University where he has worked for 40 years and from which he will retire in August 2007. While at Adelphi, he supervised numerous Master’s theses and taught courses that run the gamut from marine biology to electron microscopy. His research work focused initially on the ecology of the marine alga Codium fragile, which at the time was a relative newcomer to the East coast and of some environmental concern. In the mid-1970’s and supported by New York Sea Grant, he embarked on efforts to stabilize subtidal dredge spoil in Great South Bay via the transplantation of eelgrass. The potential significance of transplanting seagrasses was well appreciated at the time, but different methods were in the early stages of testing. While the results of the plantings were initially encouraging, their near total demise within 15 months reflects familiar experiences, even today, with transplant efforts. Subsequent work and also funded in part by New York Sea Grant included the study of heavy metal mobilization by eelgrass shoots, a description of anthesis and seed production in plants from Great South Bay, field studies on eelgrass seed banks, and the seasonal timing of seed germination. More recently, he has investigated the key role of dissolved oxygen in eelgrass seedling development, and together with Wyllie-Escheverria have helped to define the variation in seed size among and within eelgrass plants from different populations. He plans to continue his research on eelgrass at Adelphi after retirement.

Dr. Bill Dennison is a Professor of Marine Science and Vice President for Science Applications at the University of Maryland Center for Environmental Science (UMCES). Dr. Dennison’s primary mission within UMCES is to coordinate the Integration and Application Network, a group of scientists committed to solving, not just studying, environmental problems. Bill rejoined UMCES in 2002 following a ten year stint at the University of Queensland in Brisbane, Australia. He originally started at UMCES (then the Center for Environmental and Estuarine Science) in 1987 as a Research Assistant Professor based at Horn Point Laboratory. In Australia, Bill worked with an active Marine Botany group at the University of Queensland. Bill obtained his academic training from Western Michigan University (B.A), the University of Alaska (M.S), The University of Chicago (Ph.D), and State University of New York at Stony Brook at Stony Brook (Postdoc). Bill began studying seagrasses for his MS in Alaska in 1978, did his PhD research in Woods Hole, and then joined Stony Brook to study Long Island seagrasses. However, the “brown tide” algal blooms changed his focus, and the seagrass research effort was confined to documenting the brown tide impacts and studying Caribbean seagrasses. Bill is currently working with an international group of seagrass scientists through the National Center for Ecological Analysis and Synthesis on global trajectories of seagrasses, building a global seagrass database, writing a series of scientific papers and producing a suite of science communication products to raise the profile of seagrasses and seagrass conservation.

Mark S. Fonseca is the Chief of the Applied Ecology and Restoration Research Branch of NOS/NOAA, National Centers for Coastal Ocean Science, Center for Coastal Fisheries and Habitat Research in

11 Beaufort, North Carolina. Research: Project leader in basic and applied studies of marine and estuarine ecology with a focus on ecosystem restoration and management, as well as factors influencing seagrass ecology and faunal utilization particularly in the context of hydrodynamic and landscape processes. Duties are concentrated in the area of seagrass ecology, management and restoration. Studies have focused on exploring hydrodynamic interactions with marine ecosystems at a number of scales, developing seagrass planting techniques and management strategies for seagrasses in various parts of the world. Other studies include comparisons of planted vs. natural seagrass bed functions, light limitations of seagrasses and their population ecology. Recent investigations focus on the influence of hydrodynamic and disturbance processes in the formation and maintenance of marine landscapes, living marine resource use of contrasting landscape patterns and consequences of mitigative actions in these landscapes. Modeling research includes effects of scale on habitat characterization, GIS-based spatial modeling of habitat injury recovery and application of both spatial models and economic strategies in quantifying habitat injury assessment. Other active studies include developing GIS-based operational tools for wave exposure computation, boat wake effects on estuarine environments, a tidally corrected optical water quality model, as well as study of deepwater seagrass beds of the west Florida shelf, and evaluation of the Tortugas Ecological Reserve – coral reef ecosystem. Management: Develop, transfer and assist in the implementation of management strategies for marine ecosystems, assist in damage assessment and recovery analysis as well as permit reviews and expert witness testimony for the Government. Broad discretion is given by NOAA management to define research goals and strategies, procure support, execute and publish findings.

Kenneth L. Heck, Jr. is a marine ecologist whose research has focused on plant-animal interactions in coastal wetlands, and on elucidating the importance of seagrass meadows and salt marshes in the production of finfish and shellfish. From 1976-1986 he was Assistant, and then Associate Curator, and also Director of the Patrick Center for Environmental Research at the Academy of Natural Sciences in Philadelphia. Since 1986 he has been a Senior Scientist at the Dauphin Island Sea Lab (DISL) and an Associate and Full Professor at the University of South Alabama (USA). He currently serves as Chair of University Programs at DISL and as Associate Director of the Alabama Center for Estuarine Studies at USA. Dr. Heck has edited two volumes of scholarly works and published more than 100 peer-reviewed articles. He has been appointed to editorial positions at the journal Systematic Zoology, Estuaries and Coasts and is currently Contributing Editor for the international journal Marine Ecology Progress Series. In addition, he regularly serves on review panels for a wide variety of federal agencies, including the National Science Foundation, the Environmental Protection Agency and NOAA Sea Grant. Dr. Heck received his B.S. in Biology from the University of West Florida (1970) and after serving in the U.S. Army obtained his M.S. (1973) and PhD (1976) in Biology from Florida State University.

Bradley J. Peterson received the B.S. degree in Marine Biology from the Florida Institute of Technology, Melbourne, FL, in 1989, the M.S. degree in Zoology from the University of Rhode Island in 1993, and the Ph.D. degree in Marine Science from the Dauphin Island Sea Lab / University of South Alabama in 1998. His graduate research investigated the role of suspension feeding bivalves in fertilizing seagrass productivity through their biodeposits. From 1998 to 2000, he was a Tropical Biology Post- Doctoral Scholar at the Florida International University, where he was primarily responsible for overseeing the Florida Keys National Marine Sanctuary Seagrass Status and Trends Monitoring Program. From 2000 to 2002, he was a Research Scientist at the Southeast Environmental Research Center at FIU investigating the role of the sponge communities in controlling phytoplankton blooms within Florida Bay and the concomitant effect on seagrass productivity. From 2002 to 2005, he was an Assistant Professor of Marine Science at Southampton College of Long Island University. Currently, Brad is an Assistant Professor at the Marine Sciences Research Center of Stony Brook University. His research interests include positive biological interactions, bentho-pelagic coupling, ecosystem engineering, biogeochemistry of the coastal ocean, nutrient cycling in the marine environment and ecosystem modeling.

Chris Pickerell is a Habitat Restoration Specialist with Cornell University Cooperative Extension of Suffolk County. Chris has 14 years experience working on the management and restoration of salt marshes and eelgrass on Long Island. His work over the last decade has included overseeing eelgrass long-term monitoring and restoration efforts in the Peconic Estuary, Long Island Sound and, most recently, in the South Shore Estuary Reserve.

Fred Short has been studying seagrasses for 30 years, starting in the eelgrass ponds of Rhode Island and later including work in Texas, Alaska, Florida, and throughout New England. He is the founding director of a worldwide seagrass monitoring program, SeagrassNet, which began in 2001 and now has 60 sites in 21 countries, and has traveled extensively to establish that program. He is the co-editor of Global Seagrass Research Methods (2001), the World Atlas of Seagrasses (2003) and more than 70 peer-review publications. His interests include seagrass restoration and two of his papers, particularly, address restoration issues of site selection (Short et al 2002) and success criteria (Short et al 2000). In the 1990s, Short directed a large and successful eelgrass restoration in the Great Bay Estuary on the border of New Hampshire and Maine as mitigation for a port construction project. He has conducted other eelgrass restoration projects, including New Bedford Harbor, Massachusetts and Penobscot Bay, Maine. Fred is based at the University of New Hampshire’s Jackson Estuarine Laboratory, where he is a research professor. He is also the chair of UNH’s largest Ph.D. program: Natural Resources and Earth Systems Science.

Appendix C: Presenter Bios

14 Brief Biographies of Presenters

Tom Halavik is the Acting Project Leader with the U. S. Fish and Wildlife Services’ Southern New England / New York Bight Coastal Program. Tom has served as the Senior Fish and Wildlife Biologist for the Coastal Program for the last 15 years. Prior to that Tom worked as the Research Aquarium Manager and member of the Early Life History Investigation at the NOAA - National Marine Fisheries Service Laboratory in Narragansett, RI for 23 years. Tom has served as the Services’ representative to the LISS and PEP and has been an active participant on the STAC and Habitat Restoration Workgroups. He was the principal investigator for the LISS Ecological Inventory and the Inaugural Stewardship Ecological Sites as well as the PI for the PEP’s Critical Natural Resource Area designations. Tom is a USCG Licensed Captain and led the LISS Eelgrass “ground truth” efforts in 2002 and 2006.

Kimberly Petersen has a BS in Marine Science/Biology from the University of Tampa. She has worked for CCE's Marine Program since she began seasonally in 2003 and is now a year round staff member, working with Chris Pickerell and Steve Schott in the eelgrass restoration program. Kim also maintains the seagrassli.org website.

Stephen Schott has a BS in Botany and MS in Biology, specializing in marine botany and ecology, from the University of Rhode Island. He has been employed by Cornell Cooperative Extension since 2000, working with the wetland and eelgrass monitoring/restoration programs.

Christopher Clapp has been working in the Great South Bay for The Nature Conservancy since the conservancy’s efforts to restore shellfish populations in Great South Bay began in 2004. He holds an MS in Marine and Environmental Sciences form Stony Brook University’s Marine Science Research Center where he employed side-scan and multi-beam sonar to identify benthic habitats in Great South Bay.

Ron Paulsen is a Hydrogeologist with the Suffolk County Department of Health Services, Office of Water Resources. Ron has 25 years experience working on groundwater, surface water and groundwater/surface water interaction studies and investigation. Work includes investigation of various land uses (agricultural, industrial, residential) on groundwater and surface water. Several new techniques for sampling and measuring groundwater discharge have been developed in a cooperative effort with Cornell Cooperative of Suffolk and Stony Brook University. Development of an ultrasonic seepage meter and pore water sampling probes has led to new insight into the dynamic of groundwater discharge. Several studies are ongoing using these tools to characterize groundwater impacts in our local estuaries. Current work includes investigating agricultural impacts in the Peconic Estuary.

J. Kirk Cochran received his B.S. degree from Florida State University in 1973 and his Masters and Ph.D. degrees from Yale University in 1975 and 1979, respectively. He worked as a Research Staff Geologist in the Department of Geology and Geophysics at Yale University and as an Assistant Scientist in the Department of Chemistry at the Woods Hole Oceanographic Institution. Past notable appointments include Dean and Director of the Marine Sciences Research Center of Stony Brook University. Currently, Kirk is a Professor at the Marine Sciences Research Center of Stony Brook University. His research interests include marine sediment geochemistry and the use of radionuclides as geochemical tracers.

Christopher J. Gobler is an associate professor at the School of Marine and Atmospheric Sciences (SoMAS) of Stony Brook University, as well as faculty coordinator of activities for SoMAS at Stony Brook – Southampton. Prior to his appointment at Stony Brook, he was an associate professor and program coordinator of the marine sciences program for Southampton College of Long Island University. He has been researching the bays and estuaries of Long Island for more than 15 years, having published more than 30 peer reviewed scientific articles on the subject. Gobler is best known for his work on harmful algal blooms in general, and brown tides on Long Island in particular, and is an associate editor of the international journal published by Elsevier, Harmful Algae. Gobler is a Long Island native who received a bachelor’s degree in biology from the University of Delaware and his Master’s and Doctorate degrees from Stony Brook University.

Appendix D: List of Attendees

17 List of Attendees: New York Seagrass Experts Meeting Tuesday May 22, 2007

Meeting Participants (L to R): Front row: Jack Mattice (NY Sea Grant), Bradley Peterson (Stony Brook University), Kenneth Heck, Jr. (University of South Alabama), A. Coolidge Churchill (Adelphi University), J. Kirk Cochran (Stony Brook University), Marci Bortman (The Nature Conservancy). Middle rows: Paul Carlson (Florida Fish and Wildlife Conservation Commission), Christopher Gobler (Stony Brook University), Tom Halavik (US Fish & Wildlife Service), Corey Garza (Long Island Sound Study Office), Chris Pickerell (Cornell Cooperative Extension), Jeffrey Fullmer (South Shore Estuary Reserve Office), Fred Short (University of New Hampshire), Karen Chytalo (NYS Dept. of Environmental Conservation), Chris Clapp (The Nature Conservancy), Carol Pesch (US EPA), Kim Petersen (Cornell Cooperative Extension), Laura Stephenson (NYS Dept. of Environmental Conservation). Back row: Cornelia Schlenk (NY Sea Grant), Mark Fonseca (NOAA National Ocean Service), William Dennison (University of Maryland), Steve Schott (Cornell Cooperative Extension), Carl LoBue (The Nature Conservancy), Ronald Paulsen (Suffolk County Dept. of Health Services).

18 List of Attendees: New York Seagrass Experts Meeting Tuesday May 22, 2007

Name Affiliation Phone Email Ron Paulsen SCDHS 631.852.5774 [email protected] Laura Stephenson NYSDEC/PEP 631.444.0871 [email protected] Corey Garza NOAA/LISS 203.882.6505 [email protected] Jack Mattice NYSG 631.632.6905 [email protected] Carol Pesch USEPA AED 401.782.3081 [email protected] Brad Peterson MSRC 631.632.5044 [email protected] Mark Fonseca NOAA 252.728.8729 [email protected] Bill Dennison UMCES 410.228.9250 [email protected] Chris Pickerell CCE 631.852.8660 [email protected] Fred Short UNH 603.862.5134 [email protected] Stephen Schott CCE 631.852.8660 [email protected] Carl LoBue TNC 631.367.3384 [email protected] Cornelia Schlenk NYSG 631.632.6905 [email protected] Jeff Fullmer SSER 516.398.2368 [email protected] Jerry Churchill Adelphi 516.877.4192 [email protected] Chris Clapp TNC 631.367.3384 [email protected] Kirk Cochran MSRC 631.632.8733 [email protected] Tom Halavik USFWS 401.364.9124 [email protected] Karen Chytalo NYSDEC 631.444.0430 [email protected] Kim Petersen CCE 631.852.8660 [email protected] Marci Bortman TNC 631.637.3225 [email protected] Chris Gobler SBU 631.632.5043 [email protected] Ken Heck Dauphin Island 251.860.2533 [email protected] Sea Lab Paul Carlson Florida Fish and 727-896-8626 [email protected] Wildlife Research Institute

SCDHS- Suffolk County Department of Health Services NYSDEC- New York State Department of Environmental Conservation PEP- Peconic Estuary Program NOAA- National Oceanic and Atmospheric Administration LISS- Long Island Sound Study NYSG- New York Sea Grant USEPA- United State Environmental Protection Agency AED- Atlantic Ecology Division MSRC- Marine Sciences Research Center (SUNY Stony Brook) UMCES- University of Maryland Center for Environmental Science CCE- Cornell Cooperative Extension UNH- University of New Hampshire TNC- The Nature Conservancy SSER- South Shore Estuary Reserve USFWS- United States Fish and Wildlife Service SBU- Stony Brook University

Appendix E: Presentation Abstracts and Slides

20 Water Quality in Long Island’s estuaries: South Shore Estuary Reserve, Peconic Estuary, and Long Island Sound Chris Gobler, Ph.D. Associate Professor Marine Sciences Research Center, Stony Brook University

Long Island’s primary estuaries are Long Island Sound, which is bordered by Connecticut to its north and Long Island to its south, the south shore estuary system (Great South Bay, Moriches Bay, and Shinnecock Bay), which consists of barrier island estuaries along the Island’s south shore, and the Peconic Estuary, which is situated between the north and south forks of Long Island. The water quality of each estuarine system is extremely different with differing consequences for native eelgrass populations. The south shore estuaries are characterized by shallow depths (mean = 1.2 m) and gradients in water quality. Regions located near ocean inlets are cool, salty, clear, and contain low levels of algal biomass, whereas back bay regions are warmer, more fresh, and more turbid with algal biomass. While the bay bottom of inlet regions receive more than 20% of surface irradiance (the level required for robust eelgrass growth), the benthos of mid-and back-bay regions are below the 20% threshold and receive less than 1% of surface irradiance during intense algal blooms which can be common there. The Peconic Estuary contains strong gradients in depth and water clarity, with the western extreme of the estuary being shallow (2 – 3 m) but turbid and the eastern portion of the estuary being clear but deep (15 – 20m). As a consequence, Flanders Bay to the west is the only sub-estuary which likely receives > 20% of surface irradiance throughout its benthos. Eastern basins of the Peconics (Great Peconic, Little Peconic, Gardiners Bay) have levels of irradiance high enough to support eelgrass growth in their shallow, nearshore regions only. Long Island Sound also displays a strong eutrophication gradient, with high levels of phytoplankton biomass and low water quality to the west in the vicinity of New York City and clearer water to the east. Long Island Sound is also an extremely deep estuary (mean = 20 m; max = 50 m). As such, only the nearshore waters and harbors of the Sound are hospitable for eelgrass growth, with a greater likelihood of clear water and high bottom irradiance in the eastern extreme of the system.

21 Water quality in Long Island’s estuaries: South shore estuary reserve, Peconic Estuary, and d ry Long Island Sound un a o stu S E nd nic la o Is ec g P on ve L er es y R ar tu Es e or Sh h ut So

Christopher J. Gobler Marine Sciences Research Center Stony Brook University ATLANTIC OCEAN

Great South Bay • Primary ocean influence is Fire Island Inlet.

• Average mean low water depth is 1.3 m (Wilson et al. d n 1991). ou S nd la Is • Residence time is up to 96 days (Wilson et al. 1991;Conley 2000). ng Shinnecock Bay Lo Moriches Bay • Phase-shifts in algal communities: Bloom-forming ‘small forms’ to diatom-based mixed assemblages.

Great South Bay

South Shore Estuary Reserve

ATLANTIC OCEAN Bellport Bay

History of Phytoplankton in Great South Bay Moriches Bay Centric diatoms & Pennate Diatoms Dinoflagellates & Nanoflagellates • Connected to Great South Bay by Narrow Bay Dinoflagellates • Smaller than GSB, similar to Shinnecock in size

• Moriches Inlet formed in 1931. Reclosed naturally in 1951.

Diatoms Chlorophytes Cryptophytes Pennate Diatoms • Reopened again in 1954 by Hurricane Edna, and made a Diatoms Flagellates Brown Tide permanent fixture with stabilizing jetties

(Stichococcus sp.) • Received heavy input of duck farm waste (Nannochloris sp.)

1950’s- 1972 1980 1985-2001 1907 Cassin 1983 George Whipple John Ryther Carpenter & Dunham 2001 1971-1974 Greenfield et al. Weaver & Lively et al. Hirshfield Lonsdale, Gobler, Cosper Greenfield, Nixon

22 1 History of Phytoplankton in Moriches Bay Historical Data Analysis Leptocylindrus, Thallasiosira, Diatoms Skeletonema Suffolk County Department of Public Health’s Water Quality Monitoring Program.

Monthly surface water samples from 1976 – Chlorophytes 2005 (30 yrs).

Temperature, Salinity, Turbidity

(Stichococcus sp.) (Nannochloris sp.) Total dissolved nitrogen & phosphorus

1950’s 1960 - 1961 Total chlorophyll a & size fractionated John Ryther Carl Lorenzen (<10µm) 1951 1954 Closure of Moriches Inlet Moriches Inlet Opened Again John H. Ryther

16 35 15 C ° 14 Temperature 31 13 Temp 12 Shinnecock Bay 27 Nitrogen 11 Moriches Bay Great South Bay 23 10 Shinnecock Bay 0 5 10 15 20 25 30 35 40 Moriches Bay Distance from inlet (km) 19 32 nitrogen (µM) Great South Bay

Salinity Mean total dissolved 30 15 28 0 5 10 15 20 25 30 35 40 Salinity Distance from inlet (km) 26 2.0 24 1.8 0 5 10 15 20 25 30 35 40 Phosphorus Distance from inlet (km) 1.6 3.5

3.0 1.4 2.5 Secchi 1.2 2.0 1.0

1.5 phosphorus (µM)

Mean total dissolved 0.8 1.0

Secchi disk depth (m) 0.5 010203040 Distance from inlet (km) 0 5 10 15 20 25 30 35 40 Distance from inlet (km)

20 Shinnecock Bay Moriches Bay Great South Bay Synechococcus sp., Picoeukaryotes,

) 15 -1 and 2-5 µm cells Total 10 chlorphyll Chl a (µg L 200,000 5 Inlet 180,000 Estuary 0 160,000 0 5 10 15 20 25 30 35 40 140,000 Distance from inlet (km) 100 -1 120,000 a Percent 100,000 80 80,000

chlorophyll Cells ml 60,000 60 < 10 um 40,000 20,000 Percent <10 µm Chl 40 0 Synechococcus sp. Picoeukaryotes 2-5 µm 20 Distance from inlet (km) 0 5 10 15 20 25 30 35 40 Distance from inlet (km)

23 2 Pigment Ratios Light in the South Shore Estuary Reserve Dennison et al. (1993): Seagrasses are sensitive indicators of declining water quality because of their high light requirements (15-25% surface irradiance).

0.35 Diatoms 10

a Chrysophytes 20% light 9 0.3 Estuaries 1% light 8 Inlets 0.25 Dinoflagellates 7 Cryptophytes 6 0.2 5 0.15 4 Maximum Depth (m) Cyanobacteria 3 depth 0.1 Chlorophytes 2 Mean 0.05 1 depth 0

Pigment : chlorophyll : chlorophyll Pigment 0 Inlets mid-bay back bay Fuco:Chla Per:Chla Zea:Chla Allo:Chla Lutein:Chla

Eelgrass distributions in SSER, Peterson surveys, 2004-2005 Shinnecock Bay

nd ou Peconic S nd la Estuary Is ng Lo

Inlet ve er es y R ar tu Es e or Sh h Great South Bay ut So

Eelgrass abundance (Braun Blanquet Score) Inlet 00.512345 ATLANTIC OCEAN

Peconic Estuary Peconic Estuary • Two month residence time of western basin

• Shallow, but more eutrophic with low water clarity / quality to the west

• Strong tidal flushing yielding high water clarity to the east; also deeper to the east

24 3 30 20 Chlorophyll a levels in the 20% light Light levels in the 25 Peconic Estuary 1% light Peconic Estuary 15 Total depth 20

15 10 Depth (m) Chl a (ug L) / 10

5 5

0 Peconic Riv Flanders Great Little Gardiners 0 Peconic Riv Flanders Bay Great Peconic Little Peconic Gardiners Bay Peconic Peconic

HABs in the Peconics Peconics, 15-year trend in chlorophyll a

30 l

r^2 = 0.1 p < 10^-12

15 Total Chlorophy Total

0 5/7/1990 1/31/1993 10/28/1995 7/24/1998 4/19/2001 1/14/2004 10/10/2006

Peconics, 20-year trend in secchi disc depths d un y = 0.0003x - 4.1323 o 20 S R2 = 0.0405 nd la Peconic Is Estuary ng Lo

ve 10 er es y R ar stu E re ho S th Secchi Depth (130) Depth Secchi u So 0 6/2/1985 11/23/1990 5/15/1996 11/5/2001 4/28/2007

ATLANTIC OCEAN

25 4 Chlorophyll a in Long Island Sound Long Island Sound

East western central eastern 45 River LIS LIS LIS • Mean depth = 20 meters 40 • Deepest = 50 meters 35

30 25 • Bottom of main basin < 1% light level 20

Chl L) a (ug/ • Shallows of western basin also probably 15

10 low light 5 • Higher light availability in eastern shallows 0 0 50 100 150 200 Distance from NYC (km)

Conclusions

• The South Shore Estuary Reserve has a mean depth of 1.2 m, but is likely light limited in regions away from inlets due to dense blooms of small phytoplankton and resuspension.

• The Peconic Estuary is shallow but turbid in the west, and clearer but deeper to the east.

• Peconic water clarity has increased during the past 20 years.

• Long Island Sound is a deep water estuary (20 – 40 m), with turbid waters to the west, but clearer waters to the east

26 5 Linking Groundwater, Pesticides and SAV’s Ron Paulsen Hydrogeologist Suffolk County Department of Health Services, Office of Water Resources

Over the last thirty years Suffolk County Department of Health Service’s Office of Water Resources has been monitoring nutrient and pesticide impacts to the ground and surface waters in Suffolk County, New York. Thousands of samples have been collected within the watershed of the Peconic Estuary over this period. In 2007 over thirty-seven different pesticides, herbicides and fungicides have been detected in groundwater in Suffolk. The ultimate fate of this pesticide-impacted groundwater is to discharge into surface water through submarine groundwater discharge (SGD). Monitoring of the near shore groundwater, offshore porewater and SGD in the Peconic Estuary has revealed that several of these pesticides and herbicides are present at levels of concern. Impacts to the phytoplankton, algae and submerged aquatic species is a distinct possibility and may explain some of the difficulties faced in restoring SAV communities and understanding the trigger mechanisms for harmful algal blooms. Although many of these pesticides have been banned decades ago in will take many years for them to be purged from the aquifer system. This passive discharge can have prolonged and significant affects on the estuary for decades to come. Currently several studies are under way in the Peconic Estuary to determine impacts of SGD on near shore environments.

27 Linking Groundwater, Pesticides & SAV’s Nitrogen & Pesticide Studies

Steve Levy LI 208 Study (1978) Suffolk County Executive Status of Aldicarb contamination (1981) Humayan J. Chaudhry, DO, MS. 8,000 aldicarb samples 1979-1980 Commissioner Department of Health Services North & South Fork Reports (1982) Assessment of nitrate, aldicarb, dichloropropane Vito Minei, P.E. Director Comprehensive Water Resources Management Study Division of Environmental Quality (1987) Nitrate & Pesticide Impacts of Agriculture (1996) 20 year (1975-1994) nitrate avg 11.3 mg/L Aldicarb, carbofuran, oxamyl concentrations declining

Ron Paulsen TCPA found in high concentrations Hydrogeologist Office of Water Resources NYSDEC Pesticide Monitoring Program 1999-2006 2 1

1996 Pesticide Reporting Law - SCDHS Annual Reports on Water Quality Monitoring Program to NYSDEC

1998 24 pesticides & metabolites identified, 8 exceed MCLs

1999 32 pesticides & metabolites detected, 10 exceed MCLs

2000 44 pesticides & metabolites detected, 12 exceed MCLs 3,143 public, private, & monitoring wells tested in Nassau & Suffolk 25.6% contained pesticides 7.8% exceed MCLs 2002 52 pesticides & metabolites identified, 13 exceed MCLs 50.6% of private wells impacted 90.7% of private wells exceeding MCLs impacted by agricultural chemicals

3 4

Recent Monitoring Program Findings Recent Monitoring Program Findings

63 Pesticide Related Compounds Detected 15 pesticide compounds exceed MCLs 46 parent compounds 50% of private wells tested 13 pesticide degradates contain one or more 1 inert ingredient (DEHP) pesticides 3 pesticide impurities, i.e., 23% of community supply perchlorate, wells contained pesticides Co-occurrence of multiple 1,2,3-trichloropropane (DCP), pesticides - 15% of private pentachlorobenzene (PCNB fungicide) wells contained 5 or more pesticide compounds New issues Imidachloprid & DEET

5 6

28 1 Land Use Impacts

Land Use # Monitoring Wells Residential 16

Lawn Care & 7 Landscapers Greenhouses 33

Golf Courses 37

Vineyards 28

Row Crop 5 8 Agriculture

Comparative Pesticide Impacts Pesticides Exceeding MCLs in LI Groundwater Percent of Monitoring Wells Containing Pesticides

100 DBCP (banned 1979) Aldicarb (banned 1980) 80 Chlordane (banned 1983) EDB (banned 1983) 60 Dinoseb (banned 1986) 100 100 1,2 DCP (banned 1987) 78 TCPA (banned 1988) 70 40 55 Alachlor (banned 1999) Metolachlor (banned 2000) 25 20 Cyanazine (banned 2002) Simazine active 0 1,2,3 TCP (contaminant) DEHP (inert ingredient) Ag tial es n rs op u Imidachloprid (Restricted 2004) Co Cr Vineyards f DEET active Reside ol reenhouses Row G G

Lawn-Landscape 9 10

Suffolk County North Fork Cross Section Pesticide Monitoring Program North Fork Cross Section Pesticide Issues Lack of MCLs – Only carbofuran of 10 most frequently detected chemicals has a specific MCL (UOC standard 50 ppb) Occurrence of multiple compounds - MCL for multiple organic compounds is 100 ppb for total POCs & UOCs (NYS Sanitary Code) Metabolites routinely detected in greater concentrations than parent compounds Alachlor & metolachlor herbicides widely applied from ~1980 through 2000 – ESA & OA metabolites were not analyzed for prior to 1999

Nitrogen Issues Private wells exceeding 10 mg/L MCL – lack of access to public water Nitrogen discharge through stream flow and groundwater underflow to estuary – algae blooms, low dissolved oxygen

11 12

29 2 North Fork Cross-Section North Fork Aquifer Cross-Section (Nitrates)

North Fork Aquifer Cross-Section Carbamates Ag Nitrogen Monitoring 1998 - 2006

Average Annual Nitrate Concentration 20

15 e r lite r p 10 17.09 18.25 16.9 ram s

g 13.35 13.38 11.785 11.62 10.35 11 m illi

0 1998 1999 2000 2001 2002 2003 2004 2005 2006

15 16

Long-term Trends in Groundwater 3

Average Total Aldicarb Concentration (when detected) 30

10 micrograms per liter

0 1 2 3 4 7 8 9 0 1 2 85 86 87 88 89 90 17 18 991 992 993 198 198 198 198 198 19 19 19 19 19 19 1 1 1 1994 1995 1996 199 199 199 200 200 200

30 3 North Fork Stream Water Quality Sampling Stations Pesticide monitoring at 16 creeks & streams discharging to the Peconic Estuary

Sta. # Stream Sta. # Stream 200010 Peconic River (gauge) 200120 Terry Creek 200160 Brushes Creek 200200 West Creek 200004 Crescent Duck Farm 200130 Reeves Creek 200170 Deep Hole Creek 200210 East Creek (Cutchogue) 200041 Meetinghouse Creek 200140 East Creek (S Jamesport) 200180 Halls Creek 200230 Pipes Creek 200110 Sawmill Creek 200150 West Drain 200190 Downs Creek 200260 Narrow River (south)

19 20

Stream analyses show herbicide cocktails North Fork Stream Water Quality (concentrations in ug/L)

Multiple pesticides/herbicides/degradates are present in March 16, 2005 Reeves Creek, Riverhead Brushes Creek, Laurel groundwater and streams discharging to Peconic Estuary alachlor OA <0.4 1.82 37 pesticide-related compounds detected in streams alachlor ESA 0.27 2.33 metolachlor OA 2.91 0.32 More frequently detected Less frequently detected metolachlor ESA 3.41 0.59 2,6-dichlorobenzamide (BAM) <0.5 3.38 aldicarb sulfoxide alachlor OA azoxystrobin terbacil 0.19 <0.5 aldicarb sulfone metolachlor chlorothalonil dichlobenil <0.2 0.5 alachlor ESA TCPA endosulfan sulfate ronstar <0.2 1.0 metolachlor ESA simazine deisopropylatrazine metolachlor 0.4 <0.2 metalaxyl 0.4 <0.2 metolachlor OA dinoseb 4,4 DDD aldicarb sulfoxide 0.71 0.15 metalaxyl BAM aldicarb sulfone 0.5 0.29

21 22

North Fork Stream Water Quality North Fork Stream Water Quality

Maximum Pesticide Concentrations in 16 North Fork Streams Discharging to Peconic Bay Average Pesticide Concentrations ( w hen detected) in 16 North Fork Stream s 10 4.5 9 8 total aldicarb 4 7 total metolachlor 3.5 6 total alachlor 3 e r r lite 5 metalaxyl p 2.5 4 2 3 ram s tot al aldicarb g

micrograms per liter per micrograms 1.5 total metolachlor 2 1 tot al alachlor 1 micro metalaxyl 0 0.5 1996 1997 1998 1999 2000 2001 2002 2003 0 1996 1997 1998 1999 2000 2001 2002 2003 23 24

31 4 Herbicide Contaminant Issues Herbicide Contaminant Issues

EPA Alachlor RED (1998) EPA Dichlobenil RED (1998) EC50 for green algae is 1.64 ug/L “Dichlobenil is toxic to non- target terrestrial and No effect level is 0.35 ug/L. aquatic plants.” “Aquatic plants may be adversely affected by alachlor in “potentially high acute risks to mollusks” groundwater, in places where groundwater discharges into surface water.” EPA Metolcachlor RED (1995) “… where groundwater discharges to surface water, metolachlor residues could present a threat to non- target plants.”

25 26

Herbicide Contaminant Issues Overall Concerns

What is the potential for •Detections of pesticides increasing herbicide cocktail in stream •Long Residual affects (Aldicarb 30 years impact) flow and groundwater •Potential significant impacts from underflow to alter bay agricultural activities that produce ecology? concentrated waste. •Community well impacts/understanding Impacts on phytoplankton SWAP •Affects of contaminated groundwater on and eelgrass? surface water •Need for cooperative effort, sound management practices and monitoring

27 28

Groundwater/Surface Water Interactions Newly Developed Equipment and Methods

Waste Site

High Tide

Tidal Mixing Zone Sea Level Push Rod Push Plume Low Tide

Fresh G r oundwa ter

ne Air Hammer g Zo ixin ity M ens Saline D Gr ound wa ter Batt. Controller Flow meter Water Sampler Logger

Funnel onductivity C Sampl er Temperat ure

32 5 Sediment Geochemistry Pertinent to Health of SAV J. Kirk Cochran, Ph.D. Professor Marine Sciences Research Center, Stony Brook University

Geochemical reactions occurring in the upper ~30 cm of marine sediments have implications for the health of submerged aquatic vegetation. In particular, bacterial oxidation of organic matter leads to the presence of solutes in pore water that are phytotoxic. Perhaps the most important of these is hydrogen sulfide, produced from reduction of seawater sulfate as organic matter is oxidized. Dissolved hydrogen sulfide can also be removed from pore water as reduced iron reacts with it to form solid phase iron sulfides. In addition, SAV is adapted to handle elevated sulfide in pore water, but multiple stressors (light penetration in water column, eutrophication) may occur that hamper the plant’s ability to moderate the effects of sulfide. This presentation reviews the available data on sulfur geochemistry in sediments of Long Island Sound, the Peconic Bay system and Great South Bay.

33 Sediment Geochemical Issues New York Sea Grant Related to Health of SAV Seagrass Workshop • Bacterial oxidation of organic matter in sediments leads to presence of solutes in pore water that are phytotoxic (e.g. sulfide) 2CH O+SO 2-Æ H S+ 2HCO - Sediment Geochemistry 2 4 2 3 • SAV adapted to handle elevated sulfide in pore water, but must consider multiple J. Kirk Cochran stressors (light penetration in water Marine Sciences Research Center column, eutrophication)

Bacterial Oxidation of Organic Matter Sulfide in Sediment Pore water Solid phase

FeS2

FeS

2- - •Sulfide produced by sulfate reduction: 2CH2O + SO4 → H2S + 2HCO3 • ΣH S represents H S, HS- and S 2 2 o Burdige Stupakopf (1993) •H2S reacts with Fe to produce FeS and utimately, FeS2 (2006)

Sediment Geochemistry in Long Long Island Sound Island’s coastal waters • Yale University (1970s) • Long Island Sound Study (1986-7) • Long Island Sound

• Peconic Bay Yale stations • South Shore Estuarine Reserve

34 1 Solid Phase Sulfur Pools FOAM (Friends of Anoxic Mud) Site 2+ Fe + H2S → FeS → FeS2

FeS FeS2

Pore Water Sulfate Pore Water Sulfide Acid volatile S, %

H S in Jamaica Bay Marshes 2 Long Island Sound

• Long Island Sound Study (1988-89)

i ii iii July 29, 2004

iv v

LISS- Sediment Oxygen Fluxes Peconic Bays

• Peconic Estuary Program (PEP)

• Zostera and ΣH2S (I. Stupakopf,1993) • Benthic Fluxes (Howes et al.1998) • Sediment radionuclides (accumulation, mixing: Cochran et al. 1995)

Cochran et al. (1991) Howes et al. (1998)

35 2 Pore water sulfide and Zostera Pore water solutes and SAV roots

Stupakopf (1993)

• Smith Point, Narrow Bay •Sampled pore water (0-6 cm) inside (dark bars) patch of Zostera and in sediment outside (light bars) of patch Stupakopf (1993) • ΣH2S inversely correlated with irradiance, significantly different inside vs. outside

Peconic Bays- Sediment Oxygen Fluxes Great South Bay • Sampling for sediment metal distributions, basic sediment properties (Schubel et al. 1980) • Large scale sampling of sediments for radionuclides (234Th, 7Be, 210Pb) for sediment dynamics (Cochran et al. 2006-)

Howes et al. (1998)

Summary

• Large scale sediment geochemical data for Long Island’s coastal waters has tended to focus on benthic fluxes • Muddy sediments sampled most often • Less emphasis on shallow water, coarse grained sediments • Few data on pore water sulfide; more on sulfate, solid phase iron sulfides

36 3 Impacts of Habitat Modification on Eelgrass Populations in New York South Shore Estuaries Brad Peterson, Ph.D. Assistant Professor Marine Sciences Research Center, Stony Brook University

Within the State of New York, there is broad recognition that action is needed to understand, protect, enhance and restore coastal ecosystems and that ecosystem-based management is the most effective approach to accomplish such action. Recently, New York passed legislation (Bill A10584B) mandating that the state begin using ecosystem-based management for its coastal and marine resources making it the second state in the U.S. to take such action. This new mandate has resource managers re-evaluating how decisions are made and what data is required to make critical regulatory choices. In an effort to understand the strength and interaction of multiple stressors on eelgrass populations in NY estuaries, the state has recently passed legislation to set up a task force to develop recommendations for regulations to improve seagrass protection, restoration, research and monitoring. The bill states “effective regulations for seagrass protection and restoration will depend greatly on the State’s ability to understand the severity of these impacts. This task force will identify and assess severity of indirect and direct threats and develop restoration goals.”

Potential stressors on eelgrass populations in NY coastal waters include habitat modification, light shading, sulfide toxicity, and increased water temperature (Fig 1). The potential consequences and mechanisms of each of these stressors on eelgrass populations will be addressed below.

Ecosystem Stressors Structure Functions Habitat modification (Loss of filter feeders) Sediment stabilitzation (reduced turbidity)

Light shading Fisheries Resource (increased phytoplankton (nursery grounds and and turbidity) Eelgrass predation refuge) Biomass Sulfide toxicity and Associated Carbon Export (decreased bioturbation Community (detrital food resource) and oxygen injection by eelgrass) Sediment oxygenation (reduced sulfide toxicity and Increasing water enhanced nutrient regeneration)) temperature (global climate change)

Figure 1. Conceptual model of NY eelgrass stressors and ecosystem functions provided by healthy eelgrass meadows.

Habitat modification resulting from fisheries related loss of suspension feeders Long Island’s south shore estuaries (LISSE) represent a series of contiguous barrier island estuaries including Great South Bay. LISSE have been documented as some of the most productive estuaries in the nation with regard to benthic and pelagic primary productivity and the harvest of shellfish (1-3). The most successful shellfishery in the LISSE has been that of the northern quahog or hard clam, Mercenaria mercenaria. During the 1970s, two out of every

37 three hard clams eaten on the east coast of the United States came from LISSE and accounted for 54% of the total US hard clam harvest (4). These peak hard clam landings were followed by a precipitous decline in clam densities, as harvest mortalities greatly exceeded natural recruitment during the 1980s (3). More recent observations suggest that current settlement, growth and survival of hard clams in the LISSE are at an unprecedented low level (5) with recent harvest levels nearly two orders of magnitude lower than that observed in the mid 1970s. Concurrently, eelgrass coverage within LISSE has declined dramatically (Dennison et al 1989).

As "ecosystem engineers," hard clams played an important role by controlling the species diversity and abundance of phytoplankton and enhancing ecosystem stability (6). The benthic environment of a healthy clam bed consists of numerous individuals that create burrows, circulate water, and translocate the primary and secondary production from the water column to the benthos. It is therefore reasonable to assume that hard clams have an important influence on eelgrass abundance and survival by oxygenating the sediments, trapping seeds and supplying organic matter and nutrients to the benthos.

Filter feeders enhance water clarity. Chesapeake Bay represents a dramatic example of how the absence of suspension feeders has changed water clarity. There, the loss of historical oyster reefs has been implicated in phytoplankton blooms, reduced water clarity, and loss of submerged aquatic vegetation (7-9). Eelgrass is extremely sensitive to light levels and oysters played the central role of transforming pelagic organic matter into benthic production and keeping the water column clear (9). That role has been lost in many east coast estuaries, but in some areas it has been replaced by introduced filter feeders. The arrival of Corbicula fluminea in the Potomac River estuary improved water clarity and allowed eelgrass to reappear in areas from which it had been absent for 50 years (10). Similarly, Poamocorbula amurensis in San Francisco Bay are reducing phytoplankton and zooplankton densities (11, 12).

During the past quarter century, changes in LISSE microalgal communities have strongly influenced SAV communities. During the 1970’s, when Long Island’s hard clam fishery was the most productive in the nation (13), eelgrass covered 40% of LISSE (1). In 1985, the first brown tide bloom of the pelagophyte, Aureococcus anophagefferens occurred in LISSE. The annual reoccurrence of these blooms in the subsequent two decades has substantially altered the ecology of these estuaries. The negative impact of A. anophagefferens on eelgrass beds is well known. The severe light attenuation which occurs during brown tides reduces light levels and thus causes the destruction of eelgrass beds (1). It has been postulated that almost all eelgrass beds in LISSE currently subsist under subsaturating light (14).

Benthic filter feeders fertilize estuarine sediments. In addition to improving water clarity, grazing activity of filter feeders elevate submerged aquatic vegetation growth and productivity by increasing the nutrients available to the rhizosphere (15-18). By removing water PHYTOPLANKTON column particulates, suspension feedings also alter the sediment characteristics. Feces and Consumed Increase of psuedofeces produced by bivalves can increase by Seagrass Suspension Release of Productivity? both sediment organic content and nutrient Feeders Feces/Pseudofeces levels in sediment pore water (Fig 2).

38 Absorption by the roots Figure 2. Conceptual model of hard clam role in elevating eelgrass productivity Previously, Peterson and Heck (1999, 2001) found that the presence of the tulip mussel, Modiolus americanus, significantly increased the sediment nutrient pool and productivity of the seagrass, Thalassia testudinum. In addition, Reusch et al. (1994) working with the blue mussel, Mytilus edulis, and eelgrass, Zostera marina, on the west coast of the U.S. found that sediment porewater concentrations of ammonium and phosphate doubled in the presence of mussels, suggesting that the mussels fertilize eelgrass growth by the deposition of feces and pseudofeces. Similarly, Reusch and Williams (1998) demonstrated that the introduced mussel, Musculista senhousia, fertilized beds of Z. marina at moderate densities of individuals in the coastal waters off San Deigo.

Benthic filter feeders influence eelgrass recruitment, germination and seedling survival. There are three possible mechanisms by which filter feeders may influence eelgrass recruitment, germination and seedling survival. First, by providing a larger boundary layer and slowing water current speed, filter feeders may increase recruitment of floating seeds whether the seeds travel singly or within detached reproductive shoots. Seed entrapment can also be facilitated by the structure bivalves provide. Seed dispersal is limited outside Zostera marina beds (~80% seeds travel within 10 m of parent plants; (19, 20) so this effect is only important when eelgrass beds are near by or during the establishment of a new population. In addition, filter feeders might provide refuge for newly dispersed seeds from crustacean seed consumers (21, 22). The second mechanism by which hard clams may enhance eelgrass reproductive success is that bivalves can provide superior conditions for seed germination by filtering seawater and increasing sediment organic content. Z. marina seed germination is dependent on burial depth with the highest germination occurring at the anaerobic / aerobic interface (23). Filter feeders can act to bury and fertilize seeds at a depth that is appropriate for germination. Finally, filter feeders can increase the survival of seedlings, which have very high mortality rates (19, 20), by increasing light levels and nutrients and by protecting against erosion and herbivory. Despite the clear bottlenecks at these stages, there is surprisingly little information about the factors influencing eelgrass bed maintenance and formation, especially as they are related to the influence of other species interactions.

Light Shading Phytoplankton abundance in LISSE. The composition and productivity of phytoplankton communities within LISSE have been well studied for over 50 yrs (2, 24-29) during which changes in microalgal communities have strongly influenced resident eelgrass communities. In the 1950’s, Ryther (1954) documented green tides of the ‘small form’ (2 - 4 μm) chlorophytes, Nannochloris sp. and Stichococcus sp. in Moriches Bay and Great South Bay (GSB). Blooms of these species lasted over six months each year (spring through fall) during which chlorophyte cell densities often exceeded 107 cells ml-1. Poor estuarine flushing and inputs of duck farm waste along affected bays were identified as factors promoting the green tides of the 1950’s (24, 30). When a channel was dredged in the late 1950s and LISSE became well flushed with ocean water, the green tide blooms terminated.

During the 1970s, phytoplankton communities documented within LISSE were markedly different from those observed in the 1950s. While “small forms” or picoplankton were present at that time, they were part of a mixed assemblage of phytoplankton. For example, Weaver and Hirshfield (1976) indicated that pennate diatoms were the most abundant phytoplankter in western GSB. Similarly, Cassin’s (1978) demonstrated that small phytoplankton (< 10 µm) represented a small portion (< 35%) of phytoplankton biomass across GSB and also noted an

39 abundance of diatom species, as well as dinoflagellates. During a 1979-1980 study, Lively et al. (1981) reported that small phytoplankton comprised approximately half of the phytoplankton biomass in GSB and that diatoms, cryptophytes and flagellates were also abundant. It was also during the 1970’s, when larger phytoplankton were more abundant and monospecific algal blooms were not reported, that hard clam landings and eelgrass bed coverage in LISSE reached maximal levels (40%; COSMA, 1985; Dennision et al., 1989).

Overharvesting was responsible for a tremendous decline in hard clam populations through the late 1970s and early 1980s (COSMA, 1985). Concurrently, the phytoplankton community in LISSE changed from the one described during the peak of the hard clam industry in the 1970s. In 1985, the first brown tide bloom of the pelagophyte, Aureococcus anophagefferens occurred in LISSE. The annual reoccurrence of these blooms in the subsequent two decades has substantially altered the ecology of these estuaries. The negative impact of Aureococcus anophagefferens on the growth and survival of eelgrass beds is well known (1, 31). The severe light attenuation which occurs during brown tides reduces benthic light levels and thus causes the destruction of eelgrass beds.

In addition to the obvious impacts of brown tide on eelgrass in LISSE, it seems those phytoplanktons which currently dominate LISSE, even when brown tide is not in bloom, may also be deleterious to eelgrass beds. While the LISSE was dominated by moderate sized phytoplankton species during the 1970s (2, 26, 27), recent data demonstrates that phytoplankton smaller than 5 μm now comprise the majority of phytoplankton biomass in these ecosystems. For example, during multiple studies we have undertaken in LISSE since 1998, we have found that small phytoplankton (< 5 µm) now dominate (up to 90%) of algal assemblages in LISSE such as Great South Bay, Quantuck Bay, and Mecox Bay (Fig 3). This is in stark contrast to earlier studies (2, 26, 27), which found a smaller percentage of “nano- phytoplankton”, despite the use of a 10 μm size cut-off to define this algal group. The dominance of small phytoplankton (< 5 μm) in phytoplankton communities within multiple LISSE sites has also been observed by other investigators using flow cytometric techniques (32).

This abundance of small phytoplankton is likely to have a negative impact on 100 eelgrass beds. Zostera typically requires 90

15 – 25% of incident light for maximal 80 growth (33) and light penetration 70 generally has the greatest ecological impact on the growth, distribution and 60 biomass of eelgrass beds (33, 34). 50 Moreover, almost all eelgrass beds in 40

LISSE currently subsist under 30 subsaturating light, and thus any 20 change in light levels in LISSE will 5 µm < a chlorophyll of Percentage impact photosynthesis and biomass of 10 existing Zostera populations (14). Since 0 coastal Atlantic Mecox Bay Great South Bay Quantuck Bay small particles tend to scatter light more Figure 3. A comparison of the percentage of chlorophyll passing through a 5 µm mesh from samples collected in the coastal Atlantic Ocean (2002), Mecox Bay (2002), Great South Bay (1998 – 2002), and Quantuck Bay (1999 – 2002). Note: Mecox Bay is a temporally open estuary on the south shore of Long Island which exchanges with the Atlantic Ocean and is located 5 km east of Shinnecock Bay than larger particles (35), the current within LISSE. abundance of picoplankton in LISSE (Fig

40 3) has likely contributed to reduced light levels and hence reduced eelgrass distribution

The most recent change in phytoplankton community structure also does not bode well for eelgrass in Long Island estuaries. During the past three summers, harmful dinoflagellates blooms caused by Cochlodinium sp. have occurred in eastern Long Island waters, including Shinnecock Bay. The extremely high biomass associated with these blooms (> 100 µg chlorophyll a L-1) results in a shading effect equal to or greater than brown tides (Gobler et al submitted). Moreover, these blooms have a direct lethal effect on shellfish. Bay scallops exposed to bloom densities of Cochlodinium sp. for one week experienced 70% mortality and a 50% decrease in growth rate relative to control treatments (Gobler et al submitted). Other filter-feeding bivalves (hard clams, oysters) also experience significantly enhanced mortality relative to control treatments (Gobler et al submitted). Clearly, these blooms will negatively impact filter feeding bivalves and as well as eelgrass.

Sulfide Toxicity Recent studies have shown that sediment sulfide concentrations can also act alone or synergistically to cause chronic, sublethal or acutely lethal stress on seagrasses (36-38). Sulfide is produced naturally in anaerobic marine sediments by heterotrophic bacteria which use sulfate as a terminal electron acceptor in breakdown of organic matter (39). Because seagrass sediments typically have high organic matter content, sulfate reduction rates in seagrass sediments are higher than in unvegetated marine sediments (36, 40). Sulfide is also a potent cytotoxin, irreversibly binding enzymes involved in electron transport for both photosynthesis and respiration (41). Sulfide also causes hypoxia in seagrass roots and rhizomes by reacting with photosynthetically-produced oxygen diffusing from leaves to below- ground tissue. Marine plants and animals vary in their ability to tolerate sulfide, using a variety of avoidance strategies to exclude sulfide and accommodation strategies to detoxify sulfide (41). However, the tolerance limits of seagrasses can be exceeded if sulfide accumulates to toxic levels in sediment porewater. The amount of sulfide which accumulates in seagrass bed sediments depends on a number of physical and chemical characteristics. Tidal currents, wave action, and sandy sediments facilitate exchange of sediment porewater with the overlying water column, resulting in oxidation or export of sulfide produced by bacteria. In contrast, sulfide concentrations are generally higher in quiescent areas with fine grained sediments. Eelgrass may be affected by both the direct and indirect sulfide toxicity effects. The direct, cytotoxic effects will result from the reaction of sulfide with enzymes required for photosynthesis and respiration. Indirect toxicity effects are caused by hypoxia when photosynthetically-produced oxygen oxidizes sulfide which enters roots and rhizomes. Oxygen production and transport within plants is the key to resistance to hypoxia and sulfide toxicity, and eelgrass survival will depend on a balance between the plant’s oxygen supply and sediment porewater sulfide (Fig 4). Any process which causes the elevation of sediment sulfide increases

41 hypoxia or sulfide toxicity in eelgrass. Sulfide toxicity can also be increased by factors which decrease eelgrass photosynthesis (e.g. reduced light levels or increased water temperature).

Temperature The Intergovernmental Panel on Climate Change (IPCC) has predicted that global temperatures may rise by as much as 6 °C over the next century (42). Temperatures in Long Island waters have increased by 1.5°C between 1976 and 2000 (43), which represents typical patterns seen in the northeast US coast. Consistent with these findings, our analysis of summer (June – August) temperatures recorded by the Suffolk County Department of Health Services, Office of Ecology, in the shallow bays of eastern Long Island, have revealed that the maximum summer temperatures have steadily increased during the past two decades (Fig 5). In addition to stress on eelgrass populations caused by light limitation, sulfide toxicity, and habitat modification, higher sustained temperatures during summer months are likely to limit the productivity and recovery of this population.

Critical thermal stress has been reported in temperate seagrasses at temperatures above 25 oC (44-46). The effects of thermal stress on photosynthesis, productivity and morphology of seagrasses have been examined (47-50). Thorhaug et al. (1978) reported that at temperatures elevated 3–4 oC above ambient, seagrasses showed evidence of reduced standing crop and productivity, and that tropical species were more tolerant than temperate species, such as eelgrass, to elevated temperature. In addition to reducing photosynthesis and productivity, high temperatures have a dramatic effect on the internal oxygen balance of eelgrass. Increasing water temperatures stimulate plant respiration more than photosynthesis, and the meristems go anoxic, even in the light, at water temperatures above >25 °C. It has been hypothesized that low meristematic oxygen content resulting from increasing water temperatures may be a key factor in observed events of seagrass die-off (51).

LITERATURE CITED 1. W. C. Dennison, G. J. Marshall, C. Wigand, in Novel Phytoplankton Blooms: Causes and Impacts of Recurrent Brown Tides and Other Unusual Blooms E. M. Cosper, V. M. Bricelj, E. J. Carpenter, Eds. (Springer-Verlag, Berlin, 1989) pp. 675-692. 2. J. S. Lively, Z. G. Kaufman, E. J. Carpenter, Estuarine Coastal and Shelf Science 16, 51 (1981). 3. COSMA, “Suffolk County's hard clam industry: An overview and an analysis of management alternatives” (MSRC, SUNY-Stony Brook Report, 1985). 4. J. L. McHugh, in The Great South Bay J. R. Schubel, T. M. Bell, H. H. Carter, Eds. (SUNY Press, 1991). 5. NYDEC, “Report of annual hard clam landings 1990-1997” (2001).

42 6. R. Dame, S. Olenin, The Comparative Role of Suspension Feeders in Aquatic Systems (NATO AWR Nida, Lithuania, October 2003). Kluwer Academic Publishers, Netherlands (2005), pp. 7. K. A. Moore, H. A. Neckles, R. J. Orth, Marine Ecology Progress Series (1996). 8. K. A. Moore, R. L. Wetzel, Journal of Experimental Marine Biology and Ecology 244, 1 (2000). 9. J. B. C. Jackson et al., Science 293, 629 (2001). 10. H. L. Phelps, Estuaries 17, 614 (1994). 11. W. J. Kimmerer, E. Gartside, J. J. Orsi, Marine Ecology Progress Series 113, 81 (1994). 12. A. D. Jassby, J. E. Cloern, B. E. Cole, Limnology and Oceanography 47, 698 (2002). 13. J. L. Mc Hugh, in The Great South Bay J. R. Schubel, T. M. Bell, H. H. Carter, Eds. (SUNY Press, 1991). 14. S. Findlay, in Impacts of Barrier Island Breaches on Selected Biological Resources of Great South Bay, NY J. Tanski, H. Bokuniewicz, C. Schlenk, Eds. (NY Sea Grant report NYSGI-01-002, 2001). 15. T. B. H. Reusch, A. R. O. Chapman, J. P. Groger, Marine Ecology Progress Series 108, 265 (1994). 16. T. B. H. Reusch, S. L. Williams, Oecologia 113, 428 (1998). 17. B. J. Peterson, K. L. Heck, Jr., Journal of Experimental Marine Biology and Ecology 240, 37 (1999). 18. B. J. Peterson, K. L. Heck, Jr., Marine Ecology Progress Series 213, 143 (2001). 19. R. J. Orth, M. W. Luckenbach, K. A. Moore, Ecology 75, 1927 (1994). 20. M. H. Ruckelshaus, Evolution 50, 856 (1996). 21. C. Wigand, A. C. Churchill, Estuaries 11, 180 (1988). 22. J. R. Fisherman, R. J. Orth, Journal of Experimental Marine Biology and Ecology 198, 11 (1996). 23. R. E. Bigley, University of British Columbia (1981). 24. J. H. Ryther, Biological Bulletin 106, 198 (1954). 25. J. H. Ryther, W. M. Dunstan, Science 171, 1008 (1971). 26. S. S. Weaver, H. I. Hirschfield, Marine Biology 34, 273 (1976). 27. J. Cassin, Bulletin of the Torrey Botanical Club 105, 205 (1978). 28. Z. G. Kaufman, J. S. Lively, E. J. Carpenter, Estuarine Coastal and Shelf Science 17, 483 (1983). 29. C. J. Gobler, M. J. Renaghan, N. J. Buck, Limnology and Oceanography 47, 129 (2002). 30. J. H. Ryther, in Novel Phytoplankton Blooms: Causes and Impacts of Recurrent Brown Tides and Other Unususal Blooms E. M. Cosper, V. M. Bricelj, E. J. Carpenter, Eds. (Springer, New York, 1989) pp. 375-382. 31. D. I. Greenfield, D. J. Lonsdale, Marine Biology 141, 1045 (2002). 32. M. E. Sieracki, M. D. Keller, T. L. Cucci, E. Their, Transactions of the American Geophysical Union 80, 285 (1999). 33. W. C. Dennison et al., BioScience 43, 86 (1993). 34. K. L. Heck, K. W. Able, C. T. Roman, M. P. Fahay, Estuaries 18, 379 (1995). 35. A. Morel, Deep Sea Research 34, 1093 (1987). 36. P. R. Carlson, L. A. Yarbro, T. R. Barber, Bulletin of Marine Science 54, 733 (1994). 37. J. L. Goodman, K. A. Moore, W. C. Dennison, Aquatic Botany 50, 37 (1995). 38. J. M. Erskine, M. S. Koch, Aquatic Botany 67, 275 (2000). 39. M. B. Goldhaber, I. R. Kaplan, in The Sea E. D. Goldberg, Ed. (Wiley, New York, 1975), vol. 5, pp. 569-655.

43 40. M. Holmer, S. L. Nielsen, Marine Ecology Progress Series 146, 163 (1997). 41. T. Bagarinao, Aquatic Toxicology 24, 21 (1992). 42. J. T. Houghton, The science of climate change (Cambridge Press, Cambridge, 1996), pp. 43. J. J. Stachowicz, R. B. Terwin, R. B. Whitlatch, R. W. Osman, Proceedings of the National Academy of Sciences USA 99, 15497 (2002). 44. P. J. Ralph, Marine Ecology Progress Series 171, 123 (1998). 45. D. A. Bulthuis, Marine Biology Letters 4, 47 (1983). 46. A. Thorhaug, N. Blake, P. B. Schroeder, Marine Pollution Bulletin 9, 181 (1978). 47. E. A. Drew, Aquatic Botany 7, 139 (1979). 48. C. McMillan, R. C. Phillips, Aquatic Botany 7, 185 (1979). 49. C. McMillan, Aquatic Botany 17, 29 (1984). 50. D. A. Bulthuis, Aquatic Botany 27, 27 (1987). 51. T. M. Greve, J. Borum, O. Pedersen, Limnology and Oceanography 48, 210 (2003).

44 Marine Science Research Center Great South Bay Seagrass Ecology Lab

• Separated from ocean by barrier Length = 40 km island – Fire Island (150-750 m wide) Width = 2.5 – 8 km • Direct connection to ocean through Habitat modification through the Ave. depth = 1.3 m Fire Island Inlet Area = 235 km2 loss of suspension feeders • Indirect connection to ocean through RT = 54 – 84 days Jones Inlet (west) & Moriches Inlet (east)

Bradley J. Peterson

Ecosystem Stressors Structure Stressors Function Fisheries related habitat modification

1. During the 1970s, 2 out of every 3 hard clams eaten on the Habitat modification Sediment stabilization east coast of the US came from LISSE and accounted for (loss of filter feeders) (reduced turbidity) 54% of the total US hard clam harvest (McHugh, 1991). Population clearance rate ≈ 40% of the bay volume day-1 and clams exerted control on plankton assembalge (Kassner, Light Shading Eelgrass Fisheries Resource 1993) (increased phytoplankton Biomass (nursery ground and 2. These peak hard clam landings were followed by a and turbidity) predation refuge) precipitous decline in clam densities, as harvest mortalities And greatly exceeded natural recruitment during the 1980s Associated (Cosma, 1985) Carbon Export Sulfide toxicity Community 3. Most recent observations suggest that current settlement, (decreased bioturbation and (detrital food resource) growth and survival of hard clams in the LISSE are at an oxygen injection by eelgrass) unprecedented low level (NYDEC 2001) with recent harvest levels nearly two orders of magnitude lower than that observed in the mid 1970s. Under current conditions, Sediment oxygenation population clearance rate < 1% of the bay volume and clams Increasing water temperature (reduced sulfide toxicity and exert no control on plankton assemblage. (global climate change) enhanced nutrient regeneration)

Fisheries Related Habitat Modification

Time to filter GSB: GSBP 1976: 3 days

2005: > 3 months GSB76

Annual Hard Clam (Mercenaria mercenaria) Landings - Great South Bay, NY

700 600 500 400 300 Landings 200 CBO: Chesapeake Bay, Past; NB: Narangasett Bay; DB: Delaware Bay; 100 (thousands of bushels) CBP: Chesapeake Bay, Present. (From Dame, 1996) 0 1975 1980 1985 1990 1995 2000 NYDEC Data Year

1 45 Habitat Modification #1: Decrease in water clarity

1. During the 1970’s, eelgrass covered 40% of LISSE. 2. In 1985, the first brown tide bloom occurred and eelgrass coverage was reduced by 40- 50% by 1988 and more restricted to Fire Island and the western region (Dennison et al. 1989). 3. It has been postulated that almost all eelgrass beds in LISSE currently subsist under sub-saturating light (Findlay 2001).

Tank without clams Tank with clams: Brown tide densities > 10^5 Brown tide densities < 10^4

12 Consequences for light scatter 10 ) -1 8 g L

μ 1. During the 1970s, the LISSE was dominated by ( 6 a moderate sized phytoplankton species 4 Chl Water Quality 2 2. Small phytoplankton (< 5 µm) now dominate (up 0 to 90%) of algal assemblages in LISSE such as SB1 SB2 SB3 SB4 SB5 SB6 Great South Bay, Quantuck Bay, and Mecox Bay )

-1 12 A

day July 2004

Eelgrass Productivity -1 10 P<0.001 3. This abundance of small phytoplankton is likely SS -2 8 A to have a negative impact on eelgrass beds (cm AB since small particles tend to scatter light more 6 BC C than larger particles (Morel 1987) 4 C 2

0 Leaf Productivity SB1 SB2 SB3 SB4 SB5 SB6

Mesocosm Experiment Habitat Modification #2: Reduction in the translocation and burial of 100

Control Low density nutrients from the water column to the sediments 80 High density ) -1

60 g L

μ 1. Suspension feeders have been repeatedly 40 demonstrated to translocate PON, POP Chl a a ( Chl 20 from the water column to the sediment. 0 024681012 Day 2. These biodeposits increase sediment pore 0.7 1.0 y= -0.0078x + 1.0613 B water nutrient concentrations which are 2

0.6 R = 0.496 ) B

0.9 -1 0.5

) available for seagrass production.

-1 A 0.8 day d 0.4 -1 -1 0.7 ss 0.3 2 SS

0.6 2 3. Eelgrass productivity in some areas of the

(cm 0.2 Productivity

0.5 (cm 0.1 Leaf Productivity Leaf LISSE have been demonstrated to be 0.4 0.0 20 30 40 50 60 Control Low High limited by sediment nutrient availability. Mean Chl a (ug/L)

2 46 Fertilization Experiment

p < 0.001 7 B 6

) B

-1 5 A d -1 4

3 (mg SS (mg 2 SS Productivity SS 1

0 2.0 B B 1.6 A

1.2

0.8 Nitrogen (%) 0.4 Newell et al. 2002 p = 0.002 0.0 Control Fertilizer Clam

Habitat Modification #3 Habitat Modification #3 Reduction in sediment oxygenation? Reduction in sediment oxygenation?

Carlson et al., 2001

2005 Benthic Survey 2005 Benthic Survey

Sediment Organic Matter (%) EelgrassSediment abundance Organic (Braun MatterBlanquet (%) Score)

0.5 1 2 3 4 5 01357911 01357911

2 (BB score)

Eelgrass abundance (Braun Blanquet Score) Abundance Eelgrass 0 00.512345 024681012 Sediment Organic Matter (%)

3 47 (5-4-07)(5-18-07) Porewater Porewater [H2S][H2S] in GSB in GSB 16001600 Habitat Modification #4:

12001200 Reduction in seed germination and survival? 1. Seed entrapment can be facilitated by the structure a mature hard clam 800800 community provides. H2S (uM) H2S H2S (uM) 400 uM 2. Hard clams can provide superior conditions for seed germination by 400400 EC 50 P increasing sediment organic content. Zostera seed germination is dependent (*Goodman et al. 1995) on burial depth with the highest germination occurring at the anaerobic / 0 0 aerobic interface (Bigley 1981). Filter feeders can act to bury and fertilize

G P C S seeds at a depth that is appropriate for germination. 1G G H HC CS C S

G S B7 S B7 S B9 S B9 S B9 B2 G B2 G B2 G B2 G B4 G B4 G B4 G B4 G B6 G B6 G B6 G B6 G B9 GP G B9 A G B7 G B7 4 HC 4 O H H

A2 A2 G A7 3 3 GP 3 A7 SP B5 A7 SP B5 S SP B5

B5 GPB5 GPB5 GPB5 GPB8 GPB8 GSB8 B3 SO B3 SO B3 SO B3 B1 SG B1 SG B1 SG B1 A3 GP A A A A A4 HC A B10 DG A4B10 DG A6 A6

B10 S DG B10 S DG 3. Finally, filter feeders can increase the survival of seedlings, which have very STNSSTNS high mortality rates (Orth et al. 1994a; Ruckelshaus 1996), by increasing light

*Goodman, J.L. Moore, K.A., Dennison, W.C. 1995. Photosynthetic levels and nutrients and by protecting against erosion and herbivory. responses of eelgrass (Zostera marina L.) to light and sediment sulfide in a Great South Bay shallow barrier island lagoon. Aquat. Bot. 50, 37-47.

A3 A2 A7 A1 B1B2 B3 B4B5 A4 B9 A5 B8B7

1970s GSB Present GSB

Food web Food web

High Phytoplankton Biomass, Low Phytoplankton Biomass algal blooms

High filtration High Light

Low Light

O 2 Predation refuge Reduced clam Eel grass shaded out density, No oxygen (-) filtration Benthos positive No predation refuge (-) After Schramm, 1999 feedback loop Enhanced benthic nutrient flux (-) Nutrients Nutrients

4 48 Seagrass Distribution in Long Islands South Shore Bays Chris Clapp Estuary Specialist The Nature Conservancy

This presentation summarizes the current state of seagrass distribution in Long Islands South Shore Bays compares the relevant datasets available and presents data on what might be driving the trends in seagrass trends. The South Shore Bays include Hempstead Bay, South Oyster Bay, Great South Bay, Moriches Bay and Shinnecock Bay. Particular attention was focused upon the Great South Bay as there is more data available for this body of water.

The two data sets available that illustrate seagrass distribution are Data presented includes a survey performed using discreet grab samples performed by Jones and Schubel in 1979 giving the baseline of seagrass distribution for Great South Bay from the Wantagh Parkway to the Smith Point Bridge. The second dataset was supplied by the New York Department of State Office of Coastal Services and is based upon geographically referenced aerial photos taken in 2002 and includes all of the South Shore Bays. While the methods for the two datasets are very different and cannot be directly compared for trends it is possible to get a broad perspective of change between the two datasets.

The focal point of this presentation was Great South Bay. The bay was broken into townships which also correspond to geographical regions within the bay. The data revealed that seagrasses had apparently made a resurgence (~2000 acre gain) in the western bay (Town Of Babylon) and lost acreage (~5000 acre loss) in the eastern end of the bay (Town of Brookhaven), the central part of the bay (Town of Islip) remained relatively stable. While some of the discrepancy may be due to the difference in survey methods the amount of change would likely exceed the error due to methodology.

Additional data presented included sewage district maps and the out fall plants, a 2 meter contour chart, and a draft map of shoreline hardening. This data was presented to give the expert panel some background knowledge of the system and what might be contributing to or inhibiting seagrass growth.

49 South Shore Bays SAV Distribution and Trends In South Shore Bays

Shinnecock Bay

Chris Clapp, The Nature Conservancy Moriches Bay

Brad Peterson, MSRC, Stony Brook Great South Bay University Hempstead South A. Coolidge Churchill, Adelphi University Bay Oyster Bay

Source NOAA

SAV Distribution in Western Great South Bay Great South Bay Babylon Town

Area in Acres

2002 6096

1979 3913

Source data; NOAA, NYS DOS, Jones and Schubel 1979 Source data; NOAA, NYS DOS, Jones and Schubel 1979 Change 2813

Central GSB Eastern GSB Islip Town Brookhaven Town

Area in Acres Area in Acres

2002 4887 2002 3761

1979 4773 1979 8760 Source data; NOAA, NYS DOS, Jones and Schubel 1979 Change 114 Source data; NOAA, NYS DOS, Jones and Schubel 1979 Change -4999

50 1 Hempstead Bay and Moriches Bay South Oyster Bay

Area in Acres

1979 2603

2002 2520

change -83 Source data; NOAA, NYS DOS, Jones and Schubel 1979 Source data; NOAA, NYS DOS,

Shinnecock Bay Suitable Habitat

Current Seagrass coverage extends over 40-50% of all the area <2m depth Source data; NOAA, NYS DOS Source data; NOAA, NYS DOS,

Hardened Shoreline and Hardened Shoreline and Current Seagrass Distribution Current Seagrass Distribution

Source data; NOAA, NYS DOS, TNC.

51 2 Sewer Districts and Current Sewage Outfalls and Current Coverage Coverage - West

Treatment plant outfalls Treatment plant outfalls Source data; NOAA, NYS DOS, Suffolk County Dept. of Public Works

Nature Conservancy’s Nature Conservancy’s Restoration Efforts Restoration Efforts

52 3 Eelgrass Status in the Peconic Estuary: Historic vs. Present Distribution and Current Trends Steve Schott Marine Botany Educator Cornell Cooperative Extension

Prior to the implementation of the Comprehensive Conservation and Management Program (CCMP), there was no baseline data on the health or extent of eelgrass (Zostera marina L.) in the Peconic Estuary. The Long-term Eelgrass Monitoring Program (LTEMP) was initiated in 1997 to provide baseline data on several eelgrass meadows in the Estuary and continue with annual monitoring to identify trends in population dynamics and areal extent of these beds over time. In support of the LTEMP and restoration efforts, historic eelgrass coverage for the Estuary was determined using 1930 aerial photographs and compared to an aerial survey conducted in 2000. In 1930, eelgrass covered approximately 8,720 acres of the Estuary, whereas, the 2000 study found only 1,552 acres of eelgrass remained. This represents an average rate of loss of almost 100 acres per year. The trend since 2000 finds that the six LTEMP reference populations have shown a relatively steady decrease in shoot density and areal extent and, currently, two of the monitoring sites no longer support eelgrass.

53 Overview

1) Distribution of Eelgrass (Zostera marina Eelgrass Status in the Peconic L.) in the Peconic Estuary Estuary: Historic vs. Present - Historic versus Current Distribution distribution and current trends 2) PEP Long-term Eelgrass Monitoring Program Stephen Schott - Background Cornell Cooperative Extension - Methodology Marine Program - Trends

Eelgrass Distribution Eelgrass Distribution Historic vs. Present: Peconic Estuary Summary • The Peconic Estuary contained 8,720 acres of eelgrass in 1930 (This is a conservative estimate and does not include 1,990 acres of unconfirmed beds).

• The Tiner report (2003) calculated 1,552 total acres of eelgrass based on 2000 aerials, though that number is likely low as undocumented beds have since been identified.

• This represents a loss of over 80% in a 70 year period (~100 acres/year).

PEP Long-term Eelgrass Monitoring PEP Long-term Eelgrass Monitoring Program Program Background Methodology • 6 reference sites (beds), • The PEP contracted Cornell Cooperative each with 6 monitoring stations Extension, Marine Program to develop and conduct long- term eelgrass monitoring in • Eelgrass shoot density is collected from 10 randomly 1997 placed 0.10 m2 quadrats • The Program includes 6 reference beds from (Total of 60 quadrats per bed) at each station around the Estuary: Bullhead Bay (BB), Gardiners Bay (GB), Northwest Harbor (NWH), Orient Harbor • Percent cover of (OH), Southold Bay (SB) and Three Mile Harbor macroalgae, macroalgae species, and animals (TMH). observed are recorded

54 1 PEP Long-term Eelgrass Monitoring PEP Long-term Eelgrass Monitoring Program Program

Trend Analysis Summary 1) Overall, eelgrass shoot densities have been on a decline since 2000 • The major trend evident in the eelgrass data is the almost constant decline of eelgrass shoot densities in the six 2) 2002-2004 saw significant losses monitoring beds since 2000. to several beds (75% and 78% for OH and TMH, respectively) • Major declines in Bullhead Bay, Orient Harbor and Three Mile 3) 2006 found complete loss of Harbor recorded in 2004 may be linked to the severe winters eelgrass for 2 of the reference from 2002 through 2004. The extremely cold conditions froze sites (SB and TMH) and a the Estuary and resulted in ice scour in shallow areas and significant reduction in density at removal of eelgrass. Eelgrass decline in Southold Bay (2005) 2 other sites (GB and NWH) may be a result of burial by dredge spoils. 4) In 2006, BB showed a significant increase in shoot density from the • Evidence of recovery in Bullhead Bay in 2006 indicates that previous year with eelgrass re- colonizing stations that were extant beds may be able to reverse declining trends if/when unvegetated in 2005. causative pressures are relieved.

55 2 Current Management and Research Approaches Involving Eelgrass in the Peconic Estuary Kim Petersen Habitat Restoration Educator Cornell Cooperative Extension

Current Management and Research Approaches Involving Eelgrass in the Peconic Estuary includes a compilation of the following:

• Current management efforts which impact eelgrass, including local (towns bordering the Peconic Estuary) as well as state regulations. • Proposed management actions addressed in the Peconic Estuary Program Comprehensive Conservation and Management Plan. • Research which has taken place in the Peconic Estuary concerning or involving eelgrass.

Please see Appendix H.

56 2006 Eelgrass Survey for Eastern Long Island Sound Connecticut and New York Tom Halavik Senior Biologist United States Fish and Wildlife Service

The U.S. Fish and Wildlife Service’s National Wetlands Inventory Program (NWI) initiated this study in 2002 and produced a report on the distribution of eelgrass beds in the eastern portion of Long Island Sound: “Eelgrass Survey for Eastern Long Island Sound, Connecticut and New York” (Tiner, et al. 2003). This survey was intended to be the baseline study for monitoring the status of eelgrass in this area of Long Island Sound. In 2004, the U.S. Environmental Protection Agency provided funding to update this survey in 2005. This presentation outlines the methods used in the survey, summarizes inventory results, compares the findings with the 2002 survey, and provides detailed maps showing the location of eelgrass (Zostera marina) beds detected during the 2006 survey.

The project study area encompasses the eastern end of Long Island Sound, including Fishers Island and the North Fork of Long Island. It included all coastal embayments and near shore waters (i.e., to a depth of –15 feet at mean low water) bordering the Sound from Clinton Harbor to the Rhode Island border and including Fishers Island and the North Shore of Long Island from Southold to Orient Point and Plum Island. The 2006 survey located and mapped 1,905 acres of eelgrass beds in eastern Long Island Sound. Eelgrass beds were mostly present from Rocky Neck State Park east to the Rhode Island border and the north shore of Fishers Island. Four beds were found on the North Shore of Long Island, New York, with three in the Mulford Point area. No eelgrass was found from the Old Lyme Shores sub-basin to Clinton Harbor, except for two small beds (totaling 6.4 acres) associated with the Duck Island breakwater in the Duck Island Roads sub-basin The largest loss of eelgrass was observed in Mumford Cove where 11 acres disappeared (probably due to increased sedimentation).

Funding for this project was provided by the U.S. Environmental Protection Agency, Office of Ecosystem Protection, Region I. Ralph Tiner was the principal investigator for U.S. Fish and Wildlife Service (Service) and was responsible for study design, coordination, and report preparation. Herb Bergquist did the bulk of the mapping work: photo interpretation, digital database construction, and GIS processing and prepared the maps and figures. The Southern New England Estuary Program (SNEP) was responsible for field review of potential eelgrass beds, with Andrew MacLachlan and Tom Halavik taking lead roles in this effort. Aerial photography was acquired and converted to digital images by James W. Sewall Company, Old Town, Maine.

57 Eelgrass Survey for Eastern LIS 2002 & 2006

US Fish and Wildlife Service Long Island Sound • National Wetlands Inventory Program 1 Eelgrass (Zostera marina) • Southern New England Coastal Program 2

Historical Distributions, • Ralph Tiner 1,Herb Bergquist 1, Tom Halavik 2, Andrew Present Status, MacLachlan 2 Don Henne 2 Current Management and Research Approaches • Funded by the EPA Long Island Sound Study

Historical Distributions NY Historical Distributions CT

Charles Perretti, NYS DEC

LISS Habitat Restoration Manual

2006 Survey 2002 Eelgrass Survey

58 1 NOAA Coastal Change Analysis Program On The Water “Ground truth” C-Cap Protocol 2002 Pattern Recognition Environmental Considerations • Phenology • Clouds and Haze • Turbidity • Tides • Wind and Surface Waves • Sun Angle

Equipment SeaViewer U/W Video

• Color Camera Specs:

• 420 Lines of Resolution • 1.0 Lux low light sensitivity (the lower the better) • 1/3 inch Color CCD area sensor • 512(h) x 492(w) pick up area • 2 – GPS’s • -25C to +60C Operating Temperature • Color Sounder/Plotter • 78-degree Field of View Angle • Operating Voltage: DC 9.6V~12V • Coastal Radar • Power Consumption: Max 1.0 Watt • Video out: 75ohm, 1Vp-p Composite signal • SeaTracker and Monitor • Wide Angle Lens with Auto Focus & Gain • 2- VHF radios

Underwater Camera with Directional Control

Capture video or stills with Sony Digital 8 TRV740I

SEA - TRAK™ GPS Overlay

59 2 60 3 2002 – 2006 Comparisons Previous and Current Studies 1,598 acres – 1,905 acres

• Acreage Change in Sub-basin Change # of Beds • Little Narragansett Bay -2.8 -2 • Stonington Harbor +28.0 +4 • Quiambog Cove +70.7 +6 • Mystic Harbor +61.9 -- • Palmer-West Cove +0.1 -2 • Mumford Cove -11.0 -1 • Paquonock River -2.9 -1 • New London Harbor +3.9 +1 • Goshen Cove -4.9 -- • Jordan Cove -6.5 -4 • Niantic Bay +130.2 -1 • Rocky Neck State Park +7.7 -- • Duck Island Roads +5.3 -- • Fishers Island, NY +7.8 +11 • North Shore, NY +9.2 +1 • Plum Island, NY +9.5 +1 • ------• Total +306.2 +12

• Table 6. Differences in eelgrass survey results 2002-2006. + indicate gains and – losses. LISS Habitat Restoration Manual

Previous and Current Studies LISS Funded Study

Establish Restoration Objectives for Eelgrass in Long Island Sound Prepared by: University of Connecticut, Avery Point and • ZOSTERA MARINA BIBLIOGRAPHY Connecticut Department of Environmental Protection FOR THE NEERS REGION The project will focus primarily on how nutrient loading may be affecting eelgrass in Connecticut’s coves, embayments and tidal rivers and identify management measures that can be taken to restore eelgrass

61 4 Management

While deemed an “Important Habitat” in Both CT and NY there is little protection.

State •Dredging • Docks Local • Mooring and mooring fields • Shellfishing practices

62 5 A Brief History of Eelgrass Restoration on Long Island Chris Pickerell Habitat Restoration Specialist Cornell Cooperative Extension

INTRODUCTION Long Island has three distinct estuaries, Long Island Sound (LIS), Peconic Estuary (PE) and the South Shore Estuary Reserve (SSER). LIS is characteristic of southern New England estuaries with a rocky high energy shoreline, the SSER is a coastal lagoon system that has extensive shallow flats characteristic of Mid-Atlantic estuaries, and the PE has characteristics of both New England and Mid-Atlantic estuaries. Table 1 provides a qualitative assessment of typical meadow characteristics for each area. Given these differences, restoration methods vary considerably between estuaries.

Table 1. Meadow characteristics for Z. marina growing around Long Island. o Range Meadow Fetch Sediment Type Z. marina Temps. Water 1 Stressor Type Depth Clarity Long Island High- >8 Sand to Rock 0.5m to “Low” Good Disturbance Sound & Energy miles & Cobble OM South Shallow <4 Mud to Sand 0.5m to “Var” ~ WQ (Vis.) & Shore Lagoon miles ~OM 2m <28oC poor Disturbance Estuary (Waves) Reserve

Z. marina distribution in New York waters has been reduced to 10-25% of historic populations (from 1930 estimates) (Schott, pers com). In LIS and PE, eelgrass has been lost in most shallow, protected coves and harbors and retreated to deeper open waters. In the SSER, grass persists on many shallow subtidal flats. Much of the grass along the mainland shoreline in the SSER has been lost while populations ringing the north shore of the barrier island have fluctuated over the years. In some areas, meadows on these shallow sandy flat adjacent to the barrier island have expanded (e.g., parts of Shinnecock Bay).

Causes for this precipitous decline include, the wasting disease (1931), cultural eutrophication, nuisance algae blooms (i.e., “brown tide” Aureococcus anophagefferens) (1985+) and human- induced disturbance.

Extant eelgrass meadows grow subtidally in depths ranging from 0.5m to 4.5m, in mud to cobble and rock. In the early 20th century, ONE intertidal population was identified (Cold Spring Harbor), but this small meadow was lost later in the century.

There is considerable phenotypic plasticity within and between meadows depending on depth, wave exposure, light levels, bottom type, temperature and nutrient regime. Temperature appears to be a major controlling factor in these differences. Figure 1 shows a graph of typical bottom temperatures at extant meadows within each estuary. Both flowering period, and seed production can vary within and between the three estuaries (Table 2). Shoot length ranges from 20cm to 1.8meters. Epiphytic fouling varies greatly with site conditions from complete

63 fouling with macroalgae, diatoms and or bryozoans to almost nothing. There is also a distinct seasonal shift in epiphyte and drift macroalgae assemblages with changes in water temperature and light levels.

Weekly Average Water Temperatures (2006) (Long Island Eelgrass Meadows) Lagoon (Shinnecock flats, SSER) 28 Lagoon (Shinnecock Near Inlet, SSER)

Sheltered (Bullhead Bay, PE) 26 High-Energy (St. Thomas, LIS) 24

Temperature (C) 16

y a n ug p ct ct ct Jun Ju Jun -Jul -Jul -Jul ep O O -M 2 9 A S 4-Jun 1- 8- 5- 16-Jul23-Jul30 6-Aug3- 3-Sep 4- 1-O 8-Oct 5- 2- 28 1 1 2 1 20-Aug27-Aug 10-Se17-Sep2 1 2 Date

Figure 1. Weekly average water temperature (2006) for several extant eelgrass meadows around Long Island.

Table 2. Seed maturation and collection windows for eelgrass (Z. marina) meadows on Long Island, NY. Site Estuary Seeds per Peak Release & Source/Year Shoot Collection Window (Average) Smith Point South Shore 31 June 10-28 Gates/1984 Shinnecock Bay South Shore ? June 14-30 CCE /2006 South Oyster Bay South Shore 52 June 14-July 7 Gates/1984 Great South Bay South Shore 41 June 26-July 2 Churchill et al./1978

Bullhead Bay Peconic 42 June 7-14 CCE/2002 & 2006 Hallocks Bay* Peconic 36 June 24-30 CCE/2002 Noyack Creek* Peconic (107) June 24-July 7 CCE /2001& 2003 Sag Harbor Peconic 54 July 1-14 CCE/2002 Hay Beach Pt. Peconic 75 July 21-28 CCE/2003 Orient Pt. Peconic 53 July 21-Aug. 7 CCE/2001-2006

Mulford Pt. Long Island Sound 97 Aug. 7-14 CCE/2003-2006 Fishers Island Long Island Sound ~100 Aug.14-21 CCE/2004-2005 * These meadows have greatly diminished if not completely disappeared

64 EELGRASS RESTORATION ACTIVITIES BY DECADE The concept that eelgrass was something of value was first realized soon after the occurrence of the wasting disease and the resultant crash of the brant goose and bay scallop populations during the 1930’s. However, it wasn’t until the 1970’s that eelgrass restoration on Long Island really began. Prior to this, especially in Great South Bay, there was a general disregard for eelgrass as a nuisance to boaters and bathers alike. In the late 60’s the Town of Hempstead commissioned a study to determine how this species could be controlled.

1930’s The first recorded eelgrass planting effort on Long Island occurred near Jones Beach using plantings gathered from Mecox Bay (Southampton), Virginia and Washington State. Only the Washington plants survived long enough to set seed. No follow-up monitoring was conducted.

1970’s The first comprehensive restoration efforts involving eelgrass were initiated in the mid 1970’s by Dr. Jerry Churchill of Adelphi University. Churchill and a series of graduate students investigated the use whole plant transplantation as well as seeds in Great South Bay (SSER) and the Peconic Estuary. Other work involved testing various transplant methods for restoration. One important result of this work was the observation that Z. marina seeds could be transported via air bubbles. Dr. Churchill and his students also identified the most appropriate times to collect flowers to yield the most seeds.

1980’s Churchill continued work in both the SSER as well as the Peconic Estuary developing methods to use seeds for restoration. In the late 1980’s Dr. Bill Dennison, working with staff from CCE conducted a small-scale test planting of seeds in the Peconic Estuary as part of a study of the effect of brown tide on local eelgrass populations.

1990’s With the coming of the brown tide in the mid 1980’s, there was a new found interest in protecting and restoring resources in the Peconic Estuary. During the early 1990’s money was made available for various “demonstration projects” to restore resources in the PE. During the period of 1994-1999, CCE and Town of East Hampton Trustees and Natural Resources Department conducted transplants at multiple sites in town waters. Seeds were not investigated during this period. Although the results of this work were mostly discouraging, it led the way to future efforts. This was the first indication that many creeks and harbors which historically supported eelgrass may no longer be able to support this species.

2000’s After a couple year hiatus, CCE again initiated restoration activities with funding from various sources. The first projects focused on sites within the inner estuary.

2001-2004 CCE – Seeds were investigated again as a potential restoration method. Advice was sought from Dr. Jerry Churchill (Adelphi), Dr. Robert Orth (VIMS) and Steve Granger (URI). In 2002, the first Buoy Deployed Seeding (BUDS) system was constructed and deployed in the Peconic Estuary. Although this system as well as broadcast seeding produced large numbers of seedlings, long-term survival of seedlings was poor at all sites. Similar observation were made at extant meadows where natural seedling recruitment had occurred, raising questions

65 regarding the efficacy of using seeds as a primary restoration tool until the cause of these failures can be identified.

2002 CCE – Z. marina meadows “discovered” in Long Island Sound at Mulford Point, a very high energy site.

2003-2004 CCE – Based on observations at Mulford Pt., restoration site selection underwent a significant paradigm shift to high-energy, exposed sites along the LIS shore and points east in the Peconic Estuary.

2003- present CCE – Transplants were initiated in Long Island Sound and eastern Peconic Estuary with the first large-scale successes in the region. The “rock-planting” method was developed and high density, (unanchored plantings) were tested at several sites with suitable bottom conditions. Current work is conducted at the multiple-acre scale.

RESTORATION TECHNIQUES

SITE SELECTION Early restoration work on Long Island focused on the most obvious places to plant including the shallow creeks and coves where the grass most recently grew. While some of this work in the SSER was at least initially successful, most transplant and seeding efforts eventually failed. Eventually, a Transplant Suitability Index (TSI) GIS-based model was created for the PE based on the work of Dr. Fred Short (UNH) and others. This model identified eastern portions of the Estuary as the most appropriated planting areas. Verification of this model was achieved through test plantings, but physical disturbance was a confounding factor at several sites. A similar model for Shinnecock and eastern Moriches Bays is currently under development. For LIS, a Wave Exposure Model (WEMO) is being developed in collaboration with Dr. Mark Fonseca of NOAA.

RESTORATION METHODS Numerous restoration methods involving transplantation of adult shoots and seeding have been attempted on Long Island over the last 70 years. See restoration summary tables for a detailed overview of restoration activities to date. The following section covers lessons learned on Long Island.

TRANSPLANTS Successes Fall and winter plantings (mostly TERFS) were initially successful at most sheltered sites in the Peconic Estuary with survival through the winter and into the following summer. However, most transplants died by late summer.

Year-round plantings have been successful at high energy sites in Long Island Sound using the rock method.

Fall and winter plantings in Gardiners Bay have been mostly successful using high-density (200shoots/m2) 1m2 circular plots.

66 Tracking of individual plots using labeled rocks has allowed for close monitoring of factors such as donor source, planting date, weather conditions, time of year and diver error at restoration sites.

Failures Spring and summer transplants, using free-planting, the staple method and TERFS were not successful when attempted at sheltered sites within the Peconic Estuary on bottom types ranging from silty sand to sand.

SEEDS Successes Although the early seed work in the SSER did not result in meaningful establishment of plants, it did lead to an understanding and appreciation for the potential of using seeds for restoration and lead to development of flower harvest and handling methods.

Planting of seeds into sheltered embayments throughout the Peconic Estuary using the broadcast method and buoy deployed seeding indicated that seedling recruitment was not limiting to restoration efforts.

Limited success was achieved when seeding into and around existing grass at restoration sites in high-energy sites (LIS).

Failures Despite all the successes of seedling establishment in various sheltered sites (e.g., harbors and creeks) throughout the Peconic Estuary, with the exception of two sites, all seeding sites suffered catastrophic losses of shoots some time during the first summer.

Seedling recruitment never occurred in any appreciable rate at high-energy, coarse-textured sediment sites unless there were adult plants nearby.

67 A Brief History of Eelgrass in Long Island waters Eelgrass Restoration on Long Island Long Island Sound 210+ acres (USFWS)

Peconic Estuary 1,552 acres (USFWS)

South Shore Estuary Reserve 1,881 acres (total SAV) (NOAA) Chris Pickerell, CCE-Marine Program : [email protected] : www.seagrassli.org Loss of seagrass meadows around Long Island have been staggering since Email Website 1930, the year when the first comprehensive aerial photos were taken. Losses are estimated at 75-90% for the three estuaries. (S. Schott, pers. com.) Long Island Eelgrass Workshop February 15, 2007

Why is restoration necessary? Eelgrass restoration milestones on LI

LI has suffered numerous episodic losses of grass (e.g., wasting 1936 - The first documented eelgrass transplant took place near disease in 1931+ and “brown tide” 1985+) that have eliminated many Jones beach and involved planting plants from Mecox Bay, Virginia meadows in areas where conditions are still suitable for growth. and Washington in response the wasting disease of 1931.

Although many areas that have been affected by the wasting disease have recovered (except for Long Island Sound), areas impacted by 1960’s - 1970’s - In Great South Bay several researchers looked at the “brown tide” have not recovered. Is it just a matter of time? transplanting grass into various depths and bottom types. During the latter part of this period Churchill (Adelphi) was the first to investigate the use of seeds for transplants. Given the geographic and hydrological separation of extant meadows and potential restoration sites, we believe propagule limitation is preventing natural recovery in many areas. Late 1980’s - CCE organized an “Eelgrass Planting Workshop” in response to loss of grass caused by the “brown tide”. Transplant and seeding efforts were also attempted by Dennison. Restoration can overcome this and speed the process of recovery.

68 1 CCE Eelgrass Planting Workshop Eelgrass restoration milestones on LI

June 1987 1990’s - Town of East Hampton and CCE - Conducted multiple Almost exactly 20 years ago, the invited experts transplants using the staple method at several creeks and harbors. were……….. 2001-Z. marina meadows “discovered” in Long Island Sound at Mulford Point, a very high energy site. First Buoy deployed seeding line deployment.

2001 - CCE Constructs the eelgrass culture facility on Long Island at Cedar Beach, Southold.

2003 - CCE conducts first pilot seeding effort in Long Island Sound.

2003 - present - CCE begins large-scale transplants in Long Island Sound and eastern Peconic Estuary with the first large-scale successes in the region. TNC and USACOE conduct test plantings in PE and SSER. CCE refines new seeding and transplant methods (i.e., Buoy Deployed Seeding and “rock-planting”). Current work is Some things never change! conducted at the multiple-acre scale.

Eelgrass Restoration Methods Used on Eelgrass Restoration: LI Case Studies Long Island Peconic Estuary - TERFS planting X 5

During 2001 a small-scale test planting was conducted outside of Town Creek, Southold to determine the potential for large-scale restoration. 4 TERF’s were planted (61 shoots each) on 11/02/01 using plants from a nearby meadow. SEEDS Survival through winter and into the following spring was excellent. During Seed Tape (‘76) summer of 2002 the entire planting failed. Possible causes of failure include: Broadcast seeding (80’s- Present) CASE STUDIES bioturbation, high water temperatures and/or poor water clarity. Subsequent LTM Buoy Deployed Seeding (’01- Present) See Handout at Mill Creek indicated a drastic decline in the natural meadow from ~500 2 Seeds placed in burlap (’05/’06) shoots/m in 2001 to almost complete loss by 2006. TERFS (’01)

Seeding (’01) TRANSPLANTS Natural Seeding (‘04) Free-Planting (FP) (‘36 - Present) Donor Site Shelter Anchored FP (90’s) Island Rock-Planting (’04) Plugs (70’s - 90’s) 1.5miles TERFS (’01 - Present) Planting Site High-Density FP (’04 - Present) Rock-Planting (’04 - Present) May 2002 (7 months post planting)

69 2 Eelgrass Restoration: LI Case Studies Eelgrass Restoration: LI Case Studies Peconic Estuary - Seeding Peconic Estuary – Natural Seedling Recruitment On September 18th of 2001 the first attempts to deploy seeds using a floating cage (later to be called BuDS) took place at Jessups Cove, Southampton. Seedling In May 2004 evidence of a large-scale natural seeding event was documented recruitment the following spring was very good and seedlings grew rapidly. By using photographs and direct counts of individual shoots. Follow-up observations mid summer all shoots were lost. Possible causes of failure include: Shellfishing, of the site ~55 days later indicated complete loss of ALL seedlings. Similar high water temperatures and/or poor water clarity. Since that time, the donor site observations were made at another site (Bullhead Bay) in the PE that same year. at Noyack Creek has suffered periodic losses and recoveries in subsequent years. The cause of these losses are unknown, but they do not appear to be linked to In some cases large numbers of adult shoots were lost and seedling recruitment physical disturbance (i.e., bioturbation or shellfishing). was excellent only to fail in the summer.

Noyack Bay

Planting Site

Donor Site May 6, 2004 June 30, 2004 Spring 2002 (~8 months after seeding) Contour Plot (5/6/04)

Restoration Site Selection NW wind Paradigm shift (’02/’03)

New Restoration Sites Former Restoration Sites

Are these ? Creation sites?

Relative Waterquality “Historic” eelgrass distribution

Creeks & Harbors Bays & LIS Atlantic Ocean

Physical Disturbance Regime (Wave Energy)

70 3 Eelgrass Restoration: LI Case Studies St. Thomas Pt. Restoration Site, LIS Long Island Sound – Seeding and Transplants Fall 2004 plantings In October 20, 2003 the first ever seeding effort along LI’s north shore was initiated. Approximately 60,000 seeds were broadcast between two sites resulting in ONE group of plants the following season. Large-scale plantings were initiated during fall of 2005 and continued into the 2006 season. The project is a success resulting in a 2-acre meadow at St. Thomas Point and a work at Terry Point is underway to create a ¾ acre meadow. Once a canopy had formed, additional 2 years seeds were broadcast at the site and there appears to have been some natural seedling recruitment. Test plots at Terry Pt. indicate a 9-fold increase in shoot density after 13months.

Donor Sites Planting Sites

St. Thomas Pt. Dec. 2006

Eelgrass Restoration: LI Case Studies What have we learned? Shinnecock Bay – Natural Recovery 1. Each estuary is VERY different (e.g., what works in LIS As part of an Eelgrass and Bay Scallop Restoration planning project for the Town of Southampton we determined that one area in Shinnecock Bay has experienced will probably not work in the SSER). considerable natural recovery from 2001 to 2007. Comparing photo graphs of the same site indicates that seeding as well as rhizome expansion have contributed to 2. Site selection is CRITICAL and criteria need to infilling at this site, resulting in a significant increase in aerial coverage at this location. Other parts of Shinnecock bay have seen a gradual decline in aerial be refined further. coverage of grass. These observations 3. Transplants are labor intensive, but will work if done properly and at the right time of year.

4. Seeding has potential as a site selection screening tool and possibly in large-scale restoration, but additional work is necessary.

5. Initial success is no guarantee of long-term survival 2001 2007 for seeds and transplants; losses typically occur during the end of the first summer.

71 4 What have we learned? LI Eelgrass Restoration - Lessons Learned

Within-site or “mesoscale” (10’s of meters) variability Site Selection is CRITICAL: “Just because it can be considerable. used to grow there doesn’t mean it will grow there again!” • Sediment texture, fetch, wave We have to avoid the exposure, depth and other abiotic factors can vary greatly overwhelming within a site at the scale of tendency to focus 10’s of meters. only on the most obvious areas for • When designing pilot planting planting (e.g., or seeding efforts spread TEST PLOTS across depth lagoons and creeks) and bottom type changes. since they have shown to be Even if the entire site was covered with grass historically there may be only unsuitable. a small area where plantings will take (to begin the process of restoration).

What have we learned? What have we learned?

TRANSPLANTS: Labor intensive, but works when SEEDS: Seeds are a natural means of meadow the site is suitable and the timing is correct. recovery that may be suited for use in restoration if the site is suitable. Criteria: < Temperatures Criteria: > Water clarity Silty Sand sediment > Water movement < Water movement < Bioturbation < Bioturbation > Grazers Summer/Fall Fall/winter planting

72 5 What’s Next?

THE END

•Expand on current successes in LIS and eastern PE. •Make additional attempts in middle PE. •Expand seeding and transplant work in the SSER.

73 6

Appendix F: Research, Management, and Monitoring Priorities

74 Research, Management, and Monitoring Priorities

Appendix G: Potential Research Questions

79 Potential Research Questions Long Island Seagrass Experts Workshop (in no particular order of importance)

Ecology Reproduction-Seeds 1. What factors affect seedling recruitment in extant meadows? 2. Why is seedling survival low at some extant meadows (e.g., Peconic Estuary sites)? 3. What is the role of the seed bank in meadow maintenance and recovery? 4. How can we better predict the timing of seed release?

Reproduction-Vegetative 5. What factors affect lateral shoot formation? 6. What factors affect below-ground biomass allocation?

Fauna-Grazers 7. What is the role of Lacuna vincta in meadow maintenance? 8. What environmental factors control the temporal and geographic aspects of Lacuna vincta’s distribution? 9. What is the role/impact of mud snails on seedling and adult shoot survival? 10. What is the role of Mute swans and other waterfowl in grazing on seagrass?

Fauna-Bioturbation 11. What is the impact of whelk feeding on grass coverage? 12. What is the impact of crab (various sp.) burrowing and feeding activities on grass coverage?

Genetics 13. Could a lack in genetic diversity or some other related genetic difference be a possible cause as to the poor viability of seagrass in the Peconic Estuary as compared to other Long Island bays?

Physical Environment 14. What is the impact of increased water temperature on eelgrass distribution? 15. What is the impact of sea level rise on eelgrass distribution? Will seagrasses keep pace with Sea Level Rise? If not, what would you recommend for seagrass restoration? 16. What is the impact of groundwater/contaminants on eelgrass distribution? In particular, herbicides like atrizene, which may be used by farmers in the Peconic Estuary watershed? 17. What are the typical trends in meadow dynamics (e.g., percent cover and shoot density) in high energy environments? 18. What impact does hydrogen sulfide and ammonia toxicity in the sediments have on survival of seedlings and adult shoots?

Management and Restoration 19. How can we better refine our restoration site selection models (especially in light of Sea Level Rise)? 20. What do we know about the relationship between nitrogen and eelgrass? 21. How much nitrogen, as a load or concentration, is too much?

80 22. Do different forms of nitrogen affect seagrass in different ways? 23. How do different characteristics (flushing, depth, etc.) of the receiving waters affect potential water quality criteria? 24. What is our understanding of the loading from the landscape? 25. What ancillary conditions or stressors (variability of nitrogen load, seasonal effects, temperature/nitrogen interplay, other factors listed under physical environment) are important? 26. Is there a potential for water quality restoration in the range of what’s needed for eelgrass? 27. How can user conflicts be resolved such that shellfishing and eelgrass restoration can co- exist? 28. How can planting methods be improved to increase success in high energy environments? 29. Is there a critical minimum size and/or density threshold for plantings to ensure survival? 30. Seagrass in the Peconic Estuary has recently disappeared from areas where it has been for decades (e.g., Hallocks Bay and Orient Harbor) although they were historically more resilient to disturbance like brown tide relative to other areas. Are there other temperate areas where there is recent, significant seagrass loss without any indication of the presence of persistent/harmful algal blooms?

Monitoring 31. What are the best indicators of meadow health? 32. What are the most appropriate monitoring protocols (methods and timing)? 33. Is the Peconic Estuary Program Long Term Monitoring program on track? 34. What are the appropriate selection criteria for establishing new sampling stations when existing stations no longer contain seagrass? 35. How long and how often should we sample declining sites?

General 36. Why is the grass in the Peconic Estuary declining at a greater rate than other estuaries on Long Island? 37. What was the historic distribution of eelgrass along Long Island’s north shore? 38. What are the specific environmental services offered by Long Island’s seagrasses? 39. What fishery and shellfishery resources are dependent on Long Island’s seagrasses? 40. What is the relationship between shoreline armoring and seagrass distribution?

Appendix H: Other Supplemental Materials

82 Long Island Estuary Systems

Long Island Sound

85 Peconic Estuary

86 South Shore Estuary Reserve

99 Long Island Estuary Systems: Snapshot

Peconic Estuary South Shore Estuary Long Island Sound Watershed Land Acres 125,783 acres 208,640 acres 10,764,800 acres Surface Water Acres 158,056 acres 110,080 acres 844,800 acres Watershed Population 100,000 winter; 280,000 summer 1,500,000 8,500,000 Flushing Times 56 days Western; 22 days Eastern Average Depth 4.7 m 1-3 m 19.2 m Secchi Depth (ft)* winter mean 9.2 4.1 min 2.0 1.0 max 25.0 11.0

sum mean 7.1 3.8 min 2.0 1.0 max 15.0 15.0 Surface Water Temperature (C)* 32F winter; 73F summer winter mean 3.2 3.4 min < 0.1 < 0.1 max 11.0 10.3 sum mean 22.4 23.8 min 15.3 16.9 max 27.8 27.8 Total Nitrogen (mg/L)* winter mean 0.21 0.37 min < 0.05 < 0.05 max 0.80 2.20

sum mean 0.28 0.41 min < 0.05 < 0.05 max 1.40 1.10 Basin Morphology 2 Separate: Peconic Bay and Gardiner's Bay Interconnected coastal bays Eastern and Western Basins Circulation Classic estuary; FW riverine and tidal influence Inlet-fed and small rivers NYC metro area FW inputs; Western tidal Eelgrass Acres Historic 1930: 8,720 Current 2001: 1,552 2006: 1,905

*Peconic mainstem stations (Flanders, Great Peconic, Little Peconic, Noyac Bay, Shelter Island Sound, Orient Harbor, NW Harbor, Gardiners Bay) 2000-2005; Great South Bay/South Shore Estuary open bay sites (no ocean or inlet) 2000-2005.

100